rm(list=ls())
setwd("/hpc/group/pbenfeylab/CheWei/COPILOT_other_projects/Dusa_hg38_p13/")

suppressPackageStartupMessages({
    library(ggplot2)
    library(reshape2)
    #library(MAST)
    library(Matrix)
    library(Seurat)
    library(parallel)
    library(plyr)
    library(scales)
    library(ROCR)
    library(tidyverse)
    library(dplyr)
    library(patchwork)
    #library(Sushi)
    library(RColorBrewer)
    library(splines)
    #library(reticulate)
    #library(SeuratData)
    #library(SeuratWrappers)
    #library(SeuratDisk)
    #library(grid)
})

#citation("Sushi")

sessionInfo()

R version 4.2.2 (2022-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: AlmaLinux 9.5 (Teal Serval)

Matrix products: default
BLAS/LAPACK: /hpc/group/pbenfeylab/ch416/miniconda3/envs/seu4/lib/libopenblasp-r0.3.21.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] splines   parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] RColorBrewer_1.1-3 patchwork_1.1.3    forcats_0.5.2      stringr_1.5.1     
 [5] dplyr_1.1.3        purrr_1.0.2        readr_2.1.3        tidyr_1.3.0       
 [9] tibble_3.2.1       tidyverse_1.3.2    ROCR_1.0-11        scales_1.2.1      
[13] plyr_1.8.9         SeuratObject_4.1.3 Seurat_4.1.1.9001  Matrix_1.5-4      
[17] reshape2_1.4.4     ggplot2_3.4.4     

loaded via a namespace (and not attached):
  [1] readxl_1.4.1           uuid_1.1-0             backports_1.4.1       
  [4] igraph_1.5.1           repr_1.1.4             lazyeval_0.2.2        
  [7] sp_2.1-1               RcppHNSW_0.5.0         listenv_0.9.0         
 [10] scattermore_1.2        digest_0.6.33          htmltools_0.5.7       
 [13] fansi_1.0.5            magrittr_2.0.3         tensor_1.5            
 [16] googlesheets4_1.0.1    cluster_2.1.4          tzdb_0.3.0            
 [19] globals_0.16.2         modelr_0.1.10          matrixStats_1.1.0     
 [22] timechange_0.1.1       spatstat.sparse_3.0-3  colorspace_2.1-0      
 [25] rvest_1.0.3            ggrepel_0.9.4          haven_2.5.1           
 [28] crayon_1.5.2           jsonlite_1.8.7         progressr_0.14.0      
 [31] spatstat.data_3.0-3    survival_3.4-0         zoo_1.8-12            
 [34] glue_1.6.2             polyclip_1.10-6        gtable_0.3.4          
 [37] gargle_1.2.1           leiden_0.4.3           future.apply_1.11.0   
 [40] abind_1.4-5            DBI_1.1.3              spatstat.random_3.2-1 
 [43] miniUI_0.1.1.1         Rcpp_1.0.11            viridisLite_0.4.2     
 [46] xtable_1.8-4           reticulate_1.34.0      htmlwidgets_1.6.2     
 [49] httr_1.4.7             ellipsis_0.3.2         ica_1.0-3             
 [52] pkgconfig_2.0.3        uwot_0.1.16            dbplyr_2.2.1          
 [55] deldir_1.0-9           utf8_1.2.4             tidyselect_1.2.0      
 [58] rlang_1.1.2            later_1.3.1            munsell_0.5.0         
 [61] cellranger_1.1.0       tools_4.2.2            cli_3.6.1             
 [64] generics_0.1.3         broom_1.0.2            ggridges_0.5.4        
 [67] evaluate_0.23          fastmap_1.1.1          goftest_1.2-3         
 [70] fs_1.6.3               fitdistrplus_1.1-11    RANN_2.6.1            
 [73] pbapply_1.7-2          future_1.33.0          nlme_3.1-162          
 [76] mime_0.12              xml2_1.3.3             compiler_4.2.2        
 [79] plotly_4.10.3          png_0.1-8              spatstat.utils_3.0-4  
 [82] reprex_2.0.2           stringi_1.8.1          RSpectra_0.16-1       
 [85] lattice_0.21-8         IRdisplay_1.1          vctrs_0.6.4           
 [88] pillar_1.9.0           lifecycle_1.0.4        spatstat.geom_3.2-7   
 [91] lmtest_0.9-40          RcppAnnoy_0.0.21       data.table_1.14.8     
 [94] cowplot_1.1.1          irlba_2.3.5.1          httpuv_1.6.12         
 [97] R6_2.5.1               promises_1.2.1         KernSmooth_2.23-20    
[100] gridExtra_2.3          parallelly_1.36.0      codetools_0.2-19      
[103] fastDummies_1.7.3      MASS_7.3-58.3          assertthat_0.2.1      
[106] withr_2.5.2            sctransform_0.4.1      hms_1.1.2             
[109] grid_4.2.2             IRkernel_1.3.1.9000    googledrive_2.0.0     
[112] Rtsne_0.16             pbdZMQ_0.3-8           spatstat.explore_3.2-5
[115] shiny_1.7.5.1          lubridate_1.9.0        base64enc_0.1-3       

# 202212 env
sessionInfo()

R version 4.2.2 (2022-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /fast/home/c/chsu/anaconda3/envs/seu4/lib/libopenblasp-r0.3.21.so

locale:
 [1] LC_CTYPE=en_US.utf-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.utf-8        LC_COLLATE=en_US.utf-8    
 [5] LC_MONETARY=en_US.utf-8    LC_MESSAGES=en_US.utf-8   
 [7] LC_PAPER=en_US.utf-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.utf-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] splines   parallel  stats4    stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] RColorBrewer_1.1-3          Sushi_1.7.1                
 [3] biomaRt_2.54.0              zoo_1.8-11                 
 [5] patchwork_1.1.2             forcats_0.5.2              
 [7] stringr_1.4.1               dplyr_1.0.10               
 [9] purrr_0.3.5                 readr_2.1.3                
[11] tidyr_1.2.1                 tibble_3.1.8               
[13] tidyverse_1.3.2             ROCR_1.0-11                
[15] scales_1.2.1                plyr_1.8.8                 
[17] SeuratObject_4.1.3          Seurat_4.3.0               
[19] Matrix_1.5-3                MAST_1.24.0                
[21] SingleCellExperiment_1.20.0 SummarizedExperiment_1.28.0
[23] Biobase_2.58.0              GenomicRanges_1.50.0       
[25] GenomeInfoDb_1.34.3         IRanges_2.32.0             
[27] S4Vectors_0.36.0            BiocGenerics_0.44.0        
[29] MatrixGenerics_1.10.0       matrixStats_0.63.0         
[31] reshape2_1.4.4              ggplot2_3.4.0              

loaded via a namespace (and not attached):
  [1] readxl_1.4.1           uuid_1.1-0             backports_1.4.1       
  [4] BiocFileCache_2.6.0    igraph_1.3.5           repr_1.1.4            
  [7] lazyeval_0.2.2         sp_1.5-1               listenv_0.8.0         
 [10] scattermore_0.8        digest_0.6.30          htmltools_0.5.3       
 [13] fansi_1.0.3            memoise_2.0.1          magrittr_2.0.3        
 [16] tensor_1.5             googlesheets4_1.0.1    cluster_2.1.4         
 [19] tzdb_0.3.0             Biostrings_2.66.0      globals_0.16.2        
 [22] modelr_0.1.10          timechange_0.1.1       spatstat.sparse_3.0-0 
 [25] prettyunits_1.1.1      colorspace_2.0-3       rappdirs_0.3.3        
 [28] blob_1.2.3             rvest_1.0.3            ggrepel_0.9.2         
 [31] haven_2.5.1            crayon_1.5.2           RCurl_1.98-1.9        
 [34] jsonlite_1.8.3         progressr_0.11.0       spatstat.data_3.0-0   
 [37] survival_3.4-0         glue_1.6.2             polyclip_1.10-4       
 [40] gtable_0.3.1           gargle_1.2.1           zlibbioc_1.44.0       
 [43] XVector_0.38.0         leiden_0.4.3           DelayedArray_0.24.0   
 [46] future.apply_1.10.0    abind_1.4-5            DBI_1.1.3             
 [49] spatstat.random_3.0-1  miniUI_0.1.1.1         Rcpp_1.0.9            
 [52] progress_1.2.2         viridisLite_0.4.1      xtable_1.8-4          
 [55] reticulate_1.26        bit_4.0.5              htmlwidgets_1.5.4     
 [58] httr_1.4.4             ellipsis_0.3.2         ica_1.0-3             
 [61] XML_3.99-0.12          pkgconfig_2.0.3        uwot_0.1.14           
 [64] dbplyr_2.2.1           deldir_1.0-6           utf8_1.2.2            
 [67] AnnotationDbi_1.60.0   tidyselect_1.2.0       rlang_1.0.6           
 [70] later_1.2.0            cachem_1.0.6           munsell_0.5.0         
 [73] cellranger_1.1.0       tools_4.2.2            cli_3.4.1             
 [76] RSQLite_2.2.18         generics_0.1.3         broom_1.0.1           
 [79] ggridges_0.5.4         evaluate_0.18          fastmap_1.1.0         
 [82] goftest_1.2-3          bit64_4.0.5            fs_1.5.2              
 [85] fitdistrplus_1.1-8     RANN_2.6.1             KEGGREST_1.38.0       
 [88] pbapply_1.6-0          future_1.29.0          nlme_3.1-160          
 [91] mime_0.12              xml2_1.3.3             compiler_4.2.2        
 [94] filelock_1.0.2         curl_4.3.3             plotly_4.10.1         
 [97] png_0.1-7              spatstat.utils_3.0-1   reprex_2.0.2          
[100] stringi_1.7.8          lattice_0.20-45        IRdisplay_1.1         
[103] vctrs_0.5.1            pillar_1.8.1           lifecycle_1.0.3       
[106] spatstat.geom_3.0-3    lmtest_0.9-40          RcppAnnoy_0.0.20      
[109] data.table_1.14.6      cowplot_1.1.1          bitops_1.0-7          
[112] irlba_2.3.5.1          httpuv_1.6.6           R6_2.5.1              
[115] promises_1.2.0.1       KernSmooth_2.23-20     gridExtra_2.3         
[118] parallelly_1.32.1      codetools_0.2-18       MASS_7.3-58.1         
[121] assertthat_0.2.1       withr_2.5.0            sctransform_0.3.5     
[124] GenomeInfoDbData_1.2.9 hms_1.1.2              grid_4.2.2            
[127] IRkernel_1.3.1.9000    googledrive_2.0.0      Rtsne_0.16            
[130] pbdZMQ_0.3-8           spatstat.explore_3.0-5 lubridate_1.9.0       
[133] shiny_1.7.3            base64enc_0.1-3       

mt.genes <- as.character(read.table("../../Source_files/kallisto-bus/gtf_files/human_mt.txt", header=F)$V1)
id2name <- read.table("../../Source_files/kallisto-bus/gtf_files/hg38_p13_gene_id_name.txt", sep="\t", header=TRUE)
tt_id <- as.character(read.table("../../CW_data/Dusa/target_transcript_id.txt", header=F)$V1)
t_id <- unique(id2name$gene_id[sort(match(tt_id, id2name$transcript_id))])
grna_anno <- read.table("../../CW_data/Dusa/gRNA_list_complete.txt", sep="\t", header=FALSE)
grna_anno <- data.frame(grna_id=grna_anno$V1, type=grna_anno$V4)
grna_anno$order <- paste0("X",seq(1,1098,1))
control_idx <- grna_anno$order[which(grna_anno$type == "non-targctrl"| grna_anno$type == "NEG-CONTROL")]
target_idx <- grna_anno$order[which(grna_anno$type != "non-targctrl" & grna_anno$type != "NEG-CONTROL")]
pr_anno <- read.table("../../CW_data/Dusa/rhapsodygRNAs_promoter500.txt", sep="\t", header=FALSE)
colnames(pr_anno) <- c("chr", "start", "end", "strand", "name", "chr_prom", "start_prom", "end_prom", "prom_name", "overlap")
pr_anno$prom_name[which(pr_anno$prom_name == "AC195454.1")] <- "LINC02265"
pr_anno$prom_name[which(pr_anno$prom_name == "UCHL1-AS1")] <- "UCHL1.AS1"
pr_anno$prom_name[which(pr_anno$prom_name == "LVCAT1")] <- "LINC02475"
pr_anno$prom_name[which(pr_anno$prom_name == "RP11-663P9.2")] <- "NDUFB4P12"
pr_anno$prom_name[which(pr_anno$prom_name == "ZBTB12P1")] <- "ZBTB12BP"

genes.bed <- read.table("../../Source_files/kallisto-bus/gtf_files/Rhapsody_genes.bed")
colnames(genes.bed) <- c("chrom", "start", "stop","gene","score","strand","type")
#genes.bed$strand <- gsub("-","-1",gsub("\\+","+1",genes.bed$strand))
genes.bed$gene[which(genes.bed$gene == "AC195454.1")] <- "LINC02265"
genes.bed$gene[which(genes.bed$gene == "UCHL1-AS1")] <- "UCHL1.AS1"
genes.bed$gene[which(genes.bed$gene == "LVCAT1")] <- "LINC02475"
genes.bed$gene[which(genes.bed$gene == "RP11-663P9.2")] <- "NDUFB4P12"
genes.bed$gene[which(genes.bed$gene == "ZBTB12P1")] <- "ZBTB12BP"
genes.bed <- rbind(genes.bed,data.frame(chrom="chr4",start=41748293,stop=41824119,gene="AC105389.3",score=".",strand="+",type="gene"))

## Merge read counts from DBEC processed matrices
#UA9 <- read.table("../../Dusa/_1_UO_AH_902FW_DBEC_MolsPerCell.csv", header=TRUE, sep=",")
#UN <-  read.table("../../Dusa/_1_Undetermined_DBEC_MolsPerCell.csv", header=TRUE, sep=",")
#rownames(UA9) <- UA9$Cell_Index
#rownames(UN) <- UN$Cell_Index
#UA9 <- UA9[,-1]
#UN <- UN[,-1]
#shared <- UN[intersect(rownames(UN),rownames(UA9)),]
#uni <- UN[rownames(UN)[!rownames(UN) %in% intersect(rownames(UN),rownames(UA9))],]
#for (i in rownames(shared)){
#    UA9[i,] <- UA9[i,] + shared[i,]
#}
#UA9_BD <- rbind(UA9, uni)
#write.table(UA9_BD, file="../../Dusa/UA9_UN_BD.csv", quote=FALSE, sep=",")

#UA9 <- read.table("../../Dusa/UO_AH_934FW_DBEC_MolsPerCell.csv", header=TRUE, sep=",")
#UN <-  read.table("../../Dusa/Undetermined2_DBEC_MolsPerCell.csv", header=TRUE, sep=",")
#rownames(UA9) <- UA9$Cell_Index
#rownames(UN) <- UN$Cell_Index
#UA9 <- UA9[,-1]
#UN <- UN[,-1]
#shared <- UN[intersect(rownames(UN),rownames(UA9)),]
#uni <- UN[rownames(UN)[!rownames(UN) %in% intersect(rownames(UN),rownames(UA9))],]
#for (i in rownames(shared)){
#    UA9[i,] <- UA9[i,] + shared[i,]
#}
#UA9_BD <- rbind(UA9, uni)
#write.table(UA9_BD, file="../../Dusa/UA9_UN_BD_2.csv", quote=FALSE, sep=",")

## Raw counts from Rhapsody
R1 <- read.table("../../Dusa/UA9_UN_BD.csv", header=TRUE, sep=",")
R1 <- t(as.matrix(R1))
R2 <- read.table("../../Dusa/UA9_UN_BD_2.csv", header=TRUE, sep=",")
R2 <- t(as.matrix(R2))

#ngenes
nrow(R1)
nrow(R2)
#ncells
ncol(R1)
ncol(R2)

1176

1176

12597

19406

rownames(R1) <- gsub("_gencode","",rownames(R1))
rownames(R2) <- gsub("_gencode","",rownames(R2))

t_id <- rev(rownames(R1))[1:78] ## 78 targeted genes
t_idx <- sort(match(t_id,rownames(R1)));
g_idx <- seq(1,nrow(R1),1)[-t_idx]
tmtx1 <- R1[t_idx,] ## gene matrix
gmtx1 <- R1[g_idx,] ## gRNA matrix
r1 <- CreateSeuratObject(counts = R1, min.cells = 1, min.features  = 1, project = "Run1", assay = "RNA")## Include features detected in at least 1 cell. Include cells where at least 1 feature is detected.
t1 <- subset(r1, features = t_id)
g1 <- subset(r1, features = rownames(gmtx1))

t_id <- rev(rownames(R2))[1:78]
t_idx <- sort(match(t_id,rownames(R2)));
g_idx <- seq(1,nrow(R2),1)[-t_idx]
tmtx2 <- R2[t_idx,]
gmtx2 <- R2[g_idx,]
r2 <- CreateSeuratObject(counts = R2, min.cells = 1, min.features  = 1, project = "Run2", assay = "RNA")
t2 <- subset(r2, features = t_id)
g2 <- subset(r2, features = rownames(gmtx2))

df <- data.frame(log10_gRNA_UMI_per_cell=log10(g1@meta.data$nCount_RNA),log10_gene_UMI_per_cell=log10(t1@meta.data$nCount_RNA))
d <- ggplot(df, aes(log10_gRNA_UMI_per_cell, log10_gene_UMI_per_cell))
d + geom_hex()+ geom_hline(yintercept=2, linetype="dashed", color = "red", size=2)+ geom_vline(xintercept=1.3, linetype="dashed", color = "red", size=2)

plot(density(log10(g1@meta.data$nCount_RNA)), main="log10_gRNA_UMI_per_cell")
abline(v = 1.3, col="red", lwd=3, lty=2)

plot(density(log10(t1@meta.data$nCount_RNA)), main="log10_gene_UMI_per_cell")
abline(v = 2, col="red", lwd=3, lty=2)

df <- data.frame(log10_gRNA_UMI_per_cell=log10(g2@meta.data$nCount_RNA),log10_gene_UMI_per_cell=log10(t2@meta.data$nCount_RNA))
d <- ggplot(df, aes(log10_gRNA_UMI_per_cell, log10_gene_UMI_per_cell))
d + geom_hex()+ geom_hline(yintercept=1.4, linetype="dashed", color = "red", size=2)+ geom_vline(xintercept=0.95, linetype="dashed", color = "red", size=2)

plot(density(log10(g2@meta.data$nCount_RNA)), main="log10_gRNA_UMI_per_cell")
abline(v = 0.95, col="red", lwd=3, lty=2)

plot(density(log10(t2@meta.data$nCount_RNA)), main="log10_gene_UMI_per_cell")
abline(v = 1.4, col="red", lwd=3, lty=2)

Warning message:
“Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.”
Warning message:
“Removed 1512 rows containing non-finite values (`stat_binhex()`).”

Warning message:
“Removed 3531 rows containing non-finite values (`stat_binhex()`).”

tmtx1 <- tmtx1[,which(log10(g1$nCount_RNA)>1.3 & log10(t1$nCount_RNA)>2)] ## gene matrix
gmtx1 <- gmtx1[,which(log10(g1$nCount_RNA)>1.3 & log10(t1$nCount_RNA)>2)] ## gRNA matrix
g1 <- CreateSeuratObject(counts = gmtx1, min.cells = 1, min.features  = 1, project = "Run1", assay = "RNA")## Include features detected in at least 1 cell. Include cells where at least 1 feature is detected.
t1 <- CreateSeuratObject(counts = tmtx1[,colnames(g1)], min.cells = 1, min.features  = 1, project = "Run1", assay = "RNA")## Include features detected in at least 1 cell. Include cells where at least 1 feature is detected.

tmtx2 <- tmtx2[,which(log10(g2$nCount_RNA)>0.95 & log10(t2$nCount_RNA)>1.4)]
gmtx2 <- gmtx2[,which(log10(g2$nCount_RNA)>0.95 & log10(t2$nCount_RNA)>1.4)]
g2 <- CreateSeuratObject(counts = gmtx2, min.cells = 1, min.features  = 1, project = "Run2", assay = "RNA")## Include features detected in at least 1 cell. Include cells where at least 1 feature is detected.
t2 <- CreateSeuratObject(counts = tmtx2[,colnames(g2)], min.cells = 1, min.features  = 1, project = "Run2", assay = "RNA")## Include features detected in at least 1 cell. Include cells where at least 1 feature is detected.

t1
g1
t2
g2

An object of class Seurat 
62 features across 6196 samples within 1 assay 
Active assay: RNA (62 features, 0 variable features)

An object of class Seurat 
1096 features across 6196 samples within 1 assay 
Active assay: RNA (1096 features, 0 variable features)

An object of class Seurat 
64 features across 10364 samples within 1 assay 
Active assay: RNA (64 features, 0 variable features)

An object of class Seurat 
1098 features across 10364 samples within 1 assay 
Active assay: RNA (1098 features, 0 variable features)

norm1 <- apply(as.matrix(g1@assays$RNA@counts),2,function(x){x/sum(x)})
plot(density(log10(as.numeric(norm1[which(norm1>0)]))), main="log10_normalized_gRNA_UMI_entries")
abline(v = -0.8, col="red", lwd=3, lty=2)

normt1 <- apply(as.matrix(t1@assays$RNA@counts),2,function(x){x/sum(x)})
plot(density(log10(as.numeric(normt1[which(normt1>0)]))), main="log10_normalized_gene_UMI_entries")
abline(v = -0.8, col="red", lwd=3, lty=2)

norm2 <- apply(as.matrix(g2@assays$RNA@counts),2,function(x){x/sum(x)})
plot(density(log10(as.numeric(norm2[which(norm2>0)]))), main="log10_normalized_gRNA_UMI_entries")
abline(v = -0.8, col="red", lwd=3, lty=2)

normt2 <- apply(as.matrix(t2@assays$RNA@counts),2,function(x){x/sum(x)})
plot(density(log10(as.numeric(normt2[which(normt2>0)]))), main="log10_normalized_gene_UMI_entries")
abline(v = -0.8, col="red", lwd=3, lty=2)

## Remove gRNA contribution (%) < 16: gRNA UMI counts/ total UMI counts per cell 
gmtx1 <- as.matrix(g1@assays$RNA@counts)
gmtx1[norm1<0.16]=0
g1 <- CreateSeuratObject(counts = gmtx1, min.cells = 1, min.features  = 1, project = "Run1", assay = "RNA")## Include features detected in at least 1 cell. Include cells where at least 1 feature is detected.
t1 <- CreateSeuratObject(counts = tmtx1[,colnames(g1)], min.cells = 1, min.features  = 1, project = "Run1", assay = "RNA")## Include features detected in at least 1 cell. Include cells where at least 1 feature is detected.

gmtx2 <- as.matrix(g2@assays$RNA@counts)
gmtx2[norm2<0.16]=0
g2 <- CreateSeuratObject(counts = gmtx2, min.cells = 1, min.features  = 1, project = "Run2", assay = "RNA")## Include features detected in at least 1 cell. Include cells where at least 1 feature is detected.
t2 <- CreateSeuratObject(counts = tmtx2[,colnames(g2)], min.cells = 1, min.features  = 1, project = "Run2", assay = "RNA")## Include features detected in at least 1 cell. Include cells where at least 1 feature is detected.

t1
g1
t2
g2

An object of class Seurat 
62 features across 6196 samples within 1 assay 
Active assay: RNA (62 features, 0 variable features)

An object of class Seurat 
1090 features across 6196 samples within 1 assay 
Active assay: RNA (1090 features, 0 variable features)

An object of class Seurat 
64 features across 10363 samples within 1 assay 
Active assay: RNA (64 features, 0 variable features)

An object of class Seurat 
1097 features across 10363 samples within 1 assay 
Active assay: RNA (1097 features, 0 variable features)

t1 <- NormalizeData(t1)
suppressWarnings(
t1 <- SCTransform(t1, assay = "RNA", new.assay.name = "SCT", verbose = FALSE)
)
g1 <- NormalizeData(g1)
suppressWarnings(
g1 <- SCTransform(g1, assay = "RNA", new.assay.name = "SCT", verbose = FALSE)
)
# Save Seurat object
save(t1,g1, file = "../../Dusa/Run1_filtered.rdata")

t2 <- NormalizeData(t2)
suppressWarnings(
t2 <- SCTransform(t2, assay = "RNA", new.assay.name = "SCT", verbose = FALSE)
)
g2 <- NormalizeData(g2)
suppressWarnings(
g2 <- SCTransform(g2, assay = "RNA", new.assay.name = "SCT", verbose = FALSE)
)
# Save Seurat object
save(t2,g2, file = "../../Dusa/Run2_filtered.rdata")

## Number of cells
ncol(t1)
ncol(g1)
ncol(t2)
ncol(g2)

6196

6196

10363

10363

load("../../Dusa/Run1_filtered.rdata")
load("../../Dusa/Run2_filtered.rdata")

t1

An object of class Seurat 
117 features across 6196 samples within 2 assays 
Active assay: SCT (55 features, 55 variable features)
 1 other assay present: RNA

t2

An object of class Seurat 
120 features across 10363 samples within 2 assays 
Active assay: SCT (56 features, 56 variable features)
 1 other assay present: RNA

## Normalized respectively
Comt <- merge(t1, y = t2, add.cell.ids = c("R1", "R2"), project = "Rhapsody")

Comt <- SCTransform(Comt,vars.to.regress="orig.ident")

Calculating cell attributes from input UMI matrix: log_umi

Variance stabilizing transformation of count matrix of size 59 by 16559

Model formula is y ~ log_umi

Get Negative Binomial regression parameters per gene

Using 56 genes, 5000 cells

  |======================================================================| 100%

Second step: Get residuals using fitted parameters for 59 genes

  |======================================================================| 100%

Computing corrected count matrix for 59 genes

  |======================================================================| 100%

Calculating gene attributes

Wall clock passed: Time difference of 4.811563 secs

Determine variable features

Place corrected count matrix in counts slot

Regressing out orig.ident

Centering data matrix

Set default assay to SCT

Comt

An object of class Seurat 
125 features across 16559 samples within 2 assays 
Active assay: SCT (59 features, 59 variable features)
 1 other assay present: RNA

## SCTransform Var regress
df <- data.frame(RNA_count=colSums(Comt@assays$SCT@data), Run=Comt$orig.ident)
ggplot(df, aes(x=RNA_count, color=Run)) +
  geom_histogram(fill="white", alpha=0.5, position="identity", bins=60)+theme_classic()+xlab("log1p(SCT normalized count)")+ylab("Cell count")+ggtitle("Normalized gene UMI per cell")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))

summary(colSums(Comt@assays$SCT@data[,which(Comt$orig.ident=="Run1")]))
summary(colSums(Comt@assays$SCT@data[,which(Comt$orig.ident=="Run2")]))

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  12.14   28.59   31.86   31.95   35.25   53.38 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  15.71   30.15   33.21   33.53   36.64   52.81 

df <- data.frame(RNA_count=colSums(Comt@assays$RNA@counts), Run=Comt$orig.ident)
ggplot(df, aes(x=RNA_count, color=Run)) +
  geom_histogram(fill="white", alpha=0.5, position="identity", bins=60)+theme_classic()+xlab("RNA raw count (UMI)")+ylab("Cell count")+ggtitle("Gene UMI per cell")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))

df <- data.frame(RNA_count=colSums(Comt@assays$RNA@data), Run=Comt$orig.ident)
ggplot(df, aes(x=RNA_count, color=Run)) +
  geom_histogram(fill="white", alpha=0.5, position="identity", bins=60)+theme_classic()+xlab("LogNormalize")+ylab("Cell count")+ggtitle("Normalized gene UMI per cell")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))

summary(colSums(t1@assays$RNA@counts))
summary(colSums(t2@assays$RNA@counts))
summary(colSums(t1@assays$RNA@data))
summary(colSums(t2@assays$RNA@data))
summary(colSums(Comt@assays$SCT@data[,which(Comt$orig.ident=="Run1")]))
summary(colSums(Comt@assays$SCT@data[,which(Comt$orig.ident=="Run2")]))

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  101.0   525.8   802.0   859.5  1127.0  3223.0 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   26.0   144.0   212.0   240.7   305.0  1582.0 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  21.41   75.93   84.12   83.63   91.67  123.69 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  28.45   80.55   88.98   88.69   97.41  133.83 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  12.14   28.59   31.86   31.95   35.25   53.38 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  15.71   30.15   33.21   33.53   36.64   52.81 

## Normalize respectively
Comg <- merge(g1, y = g2, add.cell.ids = c("R1", "R2"), project = "Rhapsody")

Comg <- SCTransform(Comg,vars.to.regress="orig.ident")

Calculating cell attributes from input UMI matrix: log_umi

Variance stabilizing transformation of count matrix of size 1086 by 16559

Model formula is y ~ log_umi

Get Negative Binomial regression parameters per gene

Using 650 genes, 5000 cells

  |======================================================================| 100%

There are 2 estimated thetas smaller than 1e-07 - will be set to 1e-07

Found 97 outliers - those will be ignored in fitting/regularization step


Second step: Get residuals using fitted parameters for 1086 genes

  |======================================================================| 100%

Computing corrected count matrix for 1086 genes

  |======================================================================| 100%

Calculating gene attributes

Wall clock passed: Time difference of 54.68452 secs

Determine variable features

Place corrected count matrix in counts slot

Regressing out orig.ident

Centering data matrix

Set default assay to SCT

Comg

An object of class Seurat 
2183 features across 16559 samples within 2 assays 
Active assay: SCT (1086 features, 1086 variable features)
 1 other assay present: RNA

## SCTransform var regress
df <- data.frame(RNA_count=colSums(Comg@assays$SCT@data), Run=Comg$orig.ident)
ggplot(df, aes(x=RNA_count, color=Run)) +
  geom_histogram(fill="white", alpha=0.5, position="identity", bins=60)+theme_classic()+xlab("log1p(SCT normalized count)")+ylab("Cell count")+ggtitle("Normalized gRNA UMI per cell")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))

summary(colSums(Comg@assays$SCT@data[,which(Comg$orig.ident=="Run1")]))
summary(colSums(Comg@assays$SCT@data[,which(Comg$orig.ident=="Run2")]))

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   4.787   5.215   5.701   5.666  20.472 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   4.111   4.564   5.070   5.088  20.044 

df <- data.frame(RNA_count=colSums(Comg@assays$RNA@counts), Run=Comg$orig.ident)
ggplot(df, aes(x=RNA_count, color=Run)) +
  geom_histogram(fill="white", alpha=0.5, position="identity", bins=60)+theme_classic()+xlab("RNA raw count (UMI)")+ylab("Cell count")+ggtitle("gRNA UMI count per cell")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))

df <- data.frame(RNA_count=colSums(Comg@assays$RNA@data), Run=Comg$orig.ident)
ggplot(df, aes(x=RNA_count, color=Run)) +
  geom_histogram(fill="white", alpha=0.5, position="identity", bins=60)+theme_classic()+xlab("LogNormalize")+ylab("Cell count")+ggtitle("Normalized gRNA UMI per cell")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))

summary(colSums(g1@assays$RNA@counts))
summary(colSums(g2@assays$RNA@counts))
summary(colSums(g1@assays$RNA@data))
summary(colSums(g2@assays$RNA@data))
summary(colSums(Comg@assays$SCT@data[,which(Comg$orig.ident=="Run1")]))
summary(colSums(Comg@assays$SCT@data[,which(Comg$orig.ident=="Run2")]))

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   11.0   114.0   232.5   310.8   417.0  2958.0 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
    4.0    38.0    75.0   108.8   142.0  1716.0 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   9.21    9.21    9.21   10.44    9.21   31.27 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   9.21    9.21    9.21   10.74    9.21   31.29 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   4.787   5.215   5.701   5.666  20.472 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   4.111   4.564   5.070   5.088  20.044 

gRNA calling

g1 <- subset(Comg, cells=colnames(Comg)[grep("^R1",colnames(Comg))])
g2 <- subset(Comg, cells=colnames(Comg)[grep("^R2",colnames(Comg))])

summary(colSums(g1@assays$SCT@data))
summary(colSums(g2@assays$SCT@data))

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   4.787   5.215   5.701   5.666  20.472 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   4.111   4.564   5.070   5.088  20.044 

t1 <- subset(Comt, cells=colnames(Comt)[grep("^R1",colnames(Comt))])
t2 <- subset(Comt, cells=colnames(Comt)[grep("^R2",colnames(Comt))])

summary(colSums(t1@assays$SCT@data))
summary(colSums(t2@assays$SCT@data))

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  12.14   28.59   31.86   31.95   35.25   53.38 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  15.71   30.15   33.21   33.53   36.64   52.81 

## Before and after normalization and gRNA thresholding 
# Raw counts
gr1 <- as.matrix(g1@assays$RNA@counts)
#threshold
gr1[gr1>0]=1
# filter out those don't have gRNA
#gr1 <- gr1[,-which(colSums(gr1)==0)]
#control cells
grc1 <- apply(gr1[sort(match(control_idx, rownames(gr1))),],2,function(x) any(x > 0)) & apply(gr1[sort(match(target_idx, rownames(gr1))),],2,function(x) all(x == 0))

gr2 <- as.matrix(g2@assays$RNA@counts)
#threshold
gr2[gr2>0]=1
# filter out those don't have gRNA
#gr2 <- gr2[,-which(colSums(gr2)==0)]
#control cells
grc2 <- apply(gr2[sort(match(control_idx, rownames(gr2))),],2,function(x) any(x > 0)) & apply(gr2[sort(match(target_idx, rownames(gr2))),],2,function(x) all(x == 0))
                                                                                              
# Raw counts with > 1 counts/gRNA threshold
grt1 <- as.matrix(g1@assays$RNA@counts)
#threshold
grt1[grt1<=1]=0                                                                                               
grt1[grt1>1]=1 
# filter out those don't have gRNA
#grt1 <- grt1[,-which(colSums(grt1)==0)]                                                                                              
#control cells
grtc1 <- apply(grt1[sort(match(control_idx, rownames(grt1))),],2,function(x) any(x > 0)) & apply(grt1[sort(match(target_idx, rownames(grt1))),],2,function(x) all(x == 0))

grt2 <- as.matrix(g2@assays$RNA@counts)
#threshold
grt2[grt2<=1]=0                                                                                               
grt2[grt2>1]=1
# filter out those don't have gRNA
#grt2 <- grt2[,-which(colSums(grt2)==0)]                                                                                                 
#control cells
grtc2 <- apply(grt2[sort(match(control_idx, rownames(grt2))),],2,function(x) any(x > 0)) & apply(grt2[sort(match(target_idx, rownames(grt2))),],2,function(x) all(x == 0))                                                                                       

# Normalized value (LogNormalize)
gnl1 <- as.matrix(g1@assays$RNA@data)
#threshold
gnl1[gnl1>0]=1
# filter out those don't have gRNA
#gnl1 <- gnl1[,-which(colSums(gnl1)==0)]                                                                                                  
#control cells
gnlc1 <- apply(gnl1[sort(match(control_idx, rownames(gnl1))),],2,function(x) any(x > 0)) & apply(gnl1[sort(match(target_idx, rownames(gnl1))),],2,function(x) all(x == 0))

gnl2 <- as.matrix(g2@assays$RNA@data)
#threshold
gnl2[gnl2>0]=1
# filter out those don't have gRNA
#gnl2 <- gnl2[,-which(colSums(gnl2)==0)]                                                                                                  
#control cells
gnlc2 <- apply(gnl2[sort(match(control_idx, rownames(gnl2))),],2,function(x) any(x > 0)) & apply(gnl2[sort(match(target_idx, rownames(gnl2))),],2,function(x) all(x == 0))   
                                                                                              
# Normalized value > 1 unit value/gRNA threshold
gnlt1 <- as.matrix(g1@assays$RNA@data)
#threshold
gnlt1[gnlt1<=1]=0                                                                                               
gnlt1[gnlt1>1]=1
# filter out those don't have gRNA
#gnlt1 <- gnlt1[,-which(colSums(gnlt1)==0)]                                                                                                 
#control cells
gnltc1 <- apply(gnlt1[sort(match(control_idx, rownames(gnlt1))),],2,function(x) any(x > 0)) & apply(gnlt1[sort(match(target_idx, rownames(gnlt1))),],2,function(x) all(x == 0))

gnlt2 <- as.matrix(g2@assays$RNA@data)
#threshold
gnlt2[gnlt2<=1]=0                                                                                               
gnlt2[gnlt2>1]=1
# filter out those don't have gRNA
#gnlt2 <- gnlt2[,-which(colSums(gnlt2)==0)]                                                                                                
#control cells
gnltc2 <- apply(gnlt2[sort(match(control_idx, rownames(gnlt2))),],2,function(x) any(x > 0)) & apply(gnlt2[sort(match(target_idx, rownames(gnlt2))),],2,function(x) all(x == 0)) 
                                                                                                 
# Normalized value (SCTrasform)
gn1 <- as.matrix(g1@assays$SCT@data)
#threshold
gn1[gn1>0]=1
# filter out those don't have gRNA
#gn1 <- gn1[,-which(colSums(gn1)==0)]                                                                                                
#control cells
gnc1 <- apply(gn1[sort(match(control_idx, rownames(gn1))),],2,function(x) any(x > 0)) & apply(gn1[sort(match(target_idx, rownames(gn1))),],2,function(x) all(x == 0))

gn2 <- as.matrix(g2@assays$SCT@data)
#threshold
gn2[gn2>0]=1
# filter out those don't have gRNA
#gn2 <- gn2[,-which(colSums(gn2)==0)]                                                                                          
#control cells
gnc2 <- apply(gn2[sort(match(control_idx, rownames(gn2))),],2,function(x) any(x > 0)) & apply(gn2[sort(match(target_idx, rownames(gn2))),],2,function(x) all(x == 0))   
                                                                                              
# Normalized value > 1 unit value/gRNA threshold
gnt1 <- as.matrix(g1@assays$SCT@data)
#threshold
gnt1[gnt1<=1]=0                                                                                               
gnt1[gnt1>1]=1
# filter out those don't have gRNA
#gnt1 <- gnt1[,-which(colSums(gnt1)==0)]                                                                                              
#control cells
gntc1 <- apply(gnt1[sort(match(control_idx, rownames(gnt1))),],2,function(x) any(x > 0)) & apply(gnt1[sort(match(target_idx, rownames(gnt1))),],2,function(x) all(x == 0))

gnt2 <- as.matrix(g2@assays$SCT@data)
#threshold
gnt2[gnt2<=1]=0                                                                                               
gnt2[gnt2>1]=1
# filter out those don't have gRNA
#gnt2 <- gnt2[,-which(colSums(gnt2)==0)]                                                                                                 
#control cells
gntc2 <- apply(gnt2[sort(match(control_idx, rownames(gnt2))),],2,function(x) any(x > 0)) & apply(gnt2[sort(match(target_idx, rownames(gnt2))),],2,function(x) all(x == 0))

dat <- data.frame(treatment=rep("Raw_1_Threshold_Run1", length(apply(gr1,2,sum))), gRNA_per_cell=apply(gr1,2,sum))
dat <- rbind(dat, data.frame(treatment=rep("Raw_1_Threshold_Run2", length(apply(gr2,2,sum))), gRNA_per_cell=apply(gr2,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("Raw_2_Threshold_Run1", length(apply(grt1,2,sum))), gRNA_per_cell=apply(grt1,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("Raw_2_Threshold_Run2", length(apply(grt2,2,sum))), gRNA_per_cell=apply(grt2,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("LogNormalized_1_Threshold_Run1", length(apply(gnl1,2,sum))), gRNA_per_cell=apply(gnl1,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("LogNormalized_1_Threshold_Run2", length(apply(gnl2,2,sum))), gRNA_per_cell=apply(gnl2,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("LogNormalized_2_Threshold_Run1", length(apply(gnlt1,2,sum))), gRNA_per_cell=apply(gnlt1,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("LogNormalized_2_Threshold_Run2", length(apply(gnlt2,2,sum))), gRNA_per_cell=apply(gnlt2,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("SCTNormalized_1_Threshold_Run1", length(apply(gn1,2,sum))), gRNA_per_cell=apply(gn1,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("SCTNormalized_1_Threshold_Run2", length(apply(gn2,2,sum))), gRNA_per_cell=apply(gn2,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("SCTNormalized_2_Threshold_Run1", length(apply(gnt1,2,sum))), gRNA_per_cell=apply(gnt1,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("SCTNormalized_2_Threshold_Run2", length(apply(gnt2,2,sum))), gRNA_per_cell=apply(gnt2,2,sum)))

dat <- within(dat, treatment <- factor(treatment, levels= c("Raw_1_Threshold_Run1","Raw_1_Threshold_Run2","Raw_2_Threshold_Run1","Raw_2_Threshold_Run2",
                                                            "LogNormalized_1_Threshold_Run1","LogNormalized_1_Threshold_Run2","LogNormalized_2_Threshold_Run1","LogNormalized_2_Threshold_Run2",
                                                            "SCTNormalized_1_Threshold_Run1","SCTNormalized_1_Threshold_Run2","SCTNormalized_2_Threshold_Run1","SCTNormalized_2_Threshold_Run2")))

options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, gRNA_per_cell)) + geom_boxplot() + theme_minimal() +
  theme(axis.text.x = element_text(angle = 75, vjust = 1, hjust = 1,size=16),axis.title.x=element_blank(),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20)) +
geom_hline(yintercept=1, linetype="dashed", 
                color = "red", size=2)

pdf("gRNA_per_cell_202212.pdf",width=6,height=6)
ggplot(dat, aes(treatment, gRNA_per_cell)) + geom_boxplot() + theme_minimal() +
  theme(axis.text.x = element_text(angle = 75, vjust = 1, hjust = 1,size=16),axis.title.x=element_blank(),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20)) +
geom_hline(yintercept=1, linetype="dashed", 
                color = "red", size=2)
dev.off()

png: 2

options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, gRNA_per_cell)) + geom_boxplot() + theme_minimal() +
  theme(axis.text.x = element_text(angle = 75, vjust = 1, hjust = 1,size=16),axis.title.x=element_blank(),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20)) + coord_cartesian(ylim = c(0, 5))

pdf("gRNA_per_cell_202212.pdf",width=6,height=6)
ggplot(dat, aes(treatment, gRNA_per_cell)) + geom_boxplot() + theme_minimal() +
  theme(axis.text.x = element_text(angle = 75, vjust = 1, hjust = 1,size=16),axis.title.x=element_blank(),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20)) + coord_cartesian(ylim = c(0, 5))
dev.off()

png: 2

cat("Raw_1_Threshold_Run1")
summary(dat[which(dat$treatment=="Raw_1_Threshold_Run1"),]$gRNA_per_cell)
cat("Raw_1_Threshold_Run2")
summary(dat[which(dat$treatment=="Raw_1_Threshold_Run2"),]$gRNA_per_cell)
cat("Raw_2_Threshold_Run1")
summary(dat[which(dat$treatment=="Raw_2_Threshold_Run1"),]$gRNA_per_cell)
cat("Raw_2_Threshold_Run2")
summary(dat[which(dat$treatment=="Raw_2_Threshold_Run2"),]$gRNA_per_cell)
cat("LogNormalized_1_Threshold_Run1")
summary(dat[which(dat$treatment=="LogNormalized_1_Threshold_Run1"),]$gRNA_per_cell)
cat("LogNormalized_1_Threshold_Run2")
summary(dat[which(dat$treatment=="LogNormalized_1_Threshold_Run2"),]$gRNA_per_cell)
cat("LogNormalized_2_Threshold_Run1")
summary(dat[which(dat$treatment=="LogNormalized_2_Threshold_Run1"),]$gRNA_per_cell)
cat("LogNormalized_2_Threshold_Run2")
summary(dat[which(dat$treatment=="LogNormalized_2_Threshold_Run2"),]$gRNA_per_cell)
cat("SCTNormalized_1_Threshold_Run1")
summary(dat[which(dat$treatment=="SCTNormalized_1_Threshold_Run1"),]$gRNA_per_cell)
cat("SCTNormalized_1_Threshold_Run2")
summary(dat[which(dat$treatment=="SCTNormalized_1_Threshold_Run2"),]$gRNA_per_cell)
cat("SCTNormalized_2_Threshold_Run1")
summary(dat[which(dat$treatment=="SCTNormalized_2_Threshold_Run1"),]$gRNA_per_cell)
cat("SCTNormalized_2_Threshold_Run2")
summary(dat[which(dat$treatment=="SCTNormalized_2_Threshold_Run2"),]$gRNA_per_cell)

Raw_1_Threshold_Run1

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   1.00    1.00    1.00    1.16    1.00    4.00 

Raw_1_Threshold_Run2

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
    1.0     1.0     1.0     1.2     1.0     4.0 

Raw_2_Threshold_Run1

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   1.00    1.00    1.00    1.16    1.00    4.00 

Raw_2_Threshold_Run2

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
    1.0     1.0     1.0     1.2     1.0     4.0 

LogNormalized_1_Threshold_Run1

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   1.00    1.00    1.00    1.16    1.00    4.00 

LogNormalized_1_Threshold_Run2

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
    1.0     1.0     1.0     1.2     1.0     4.0 

LogNormalized_2_Threshold_Run1

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   1.00    1.00    1.00    1.16    1.00    4.00 

LogNormalized_2_Threshold_Run2

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
    1.0     1.0     1.0     1.2     1.0     4.0 

SCTNormalized_1_Threshold_Run1

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   1.000   1.000   1.158   1.000   4.000 

SCTNormalized_1_Threshold_Run2

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   1.000   1.000   1.197   1.000   4.000 

SCTNormalized_2_Threshold_Run1

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   1.000   1.000   1.158   1.000   4.000 

SCTNormalized_2_Threshold_Run2

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   1.000   1.000   1.197   1.000   4.000 

apply(as.matrix(g1@assays$RNA@counts)[,colSums(grt1==1)==2],2,function(x){x[x>0]})

A matrix: 2 × 767 of type dbl

R1_669405	R1_239628	R1_150531	R1_673925	R1_174418	R1_394891	R1_879922	R1_232726	R1_645973	R1_805522	⋯	R1_535059	R1_258728	R1_383082	R1_806757	R1_190872	R1_97057	R1_267545	R1_312372	R1_804603	R1_593884
1156	1169	642	957	996	680	891	853	1021	735	⋯	18	9	13	26	17	23	6	23	6	18
971	890	520	1289	1111	893	906	1202	897	1254	⋯	30	19	16	34	26	22	27	12	29	5

Reproducibility

ep1 <- rowSums(t1@assays$RNA@data[intersect(rownames(t1),rownames(t2)),])/ncol(t1)
ep2 <- rowSums(t2@assays$RNA@data[intersect(rownames(t1),rownames(t2)),])/ncol(t2)
test <- data.frame(ep1=ep1,ep2=ep2)
mod = lm(ep1~ep2, data = test)
modsum = summary(mod)
ar2 = modsum$adj.r.squared

mod

Call:
lm(formula = ep1 ~ ep2, data = test)

Coefficients:
(Intercept)          ep2  
    0.08808      0.88425  

dat <- data.frame(ep1 = ep1, ep2 = ep2)

rsquared <- bquote(italic(R)^2 == .(format(ar2, digits = 3)))
pearsonr <- bquote(italic(r) == .(format(cor(ep1,ep2,method = "pearson"), digits = 3)))
options(repr.plot.width=8, repr.plot.height=8)
plot(ep1,ep2, xlab="Run1 pseudo-bulk expression profile ", ylab ="Run2 pseudo-bulk expression profile")
abline(lm(ep1 ~ ep2))
text(x = 200, y = 20, labels = rsquared)
text(x = 198, y = 15, labels = pearsonr)

ggplot(dat,aes(x=ep1,y=ep2))+ geom_point(size=3)+geom_abline(intercept = 0.08808, slope = 0.88425)+theme_classic()+ggtitle(bquote(.(rsquared)~.(pearsonr)))+xlab("Run1 pseudo-bulk expression profile")+ylab("Run2 pseudo-bulk expression profile")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )

pdf("Reproducibility_202212.pdf",width=6,height=6)
ggplot(dat,aes(x=ep1,y=ep2))+ geom_point(size=3)+geom_abline(intercept = 0.09127, slope = 0.87948)+theme_classic()+ggtitle(bquote(.(rsquared)~.(pearsonr)))+xlab("Run1 pseudo-bulk expression profile")+ylab("Run2 pseudo-bulk expression profile")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()

png: 2

Capture efficiency before gRNA thresholding and cell filtering

per.per.cell <- apply(gnt1,2,sum)
O <- table(per.per.cell)
loglik <- function(alpha, lambda, O) {
  krange <- as.integer(names(O))
  K <- max(krange)
sum(
  sapply(krange, function(k) O[as.character(k)] * log(sum( #k: number of guides observed
    sapply(max(c(k,1)):K, function(j) choose(j,k) * alpha ^ k * (1-alpha) ^ (j-k) * ( lambda ^ j / (factorial(j) * (exp(lambda) - 1))  )) #j: number of guides present
    )))
)
  
}
#Compiute log likelihood over parameter ranges
#moir <- seq(0,3,by=0.04)
moir <- 0.3 
alphar <- seq(0,1,by=0.001)
complete <- sapply(moir, function(moi) {
  sapply(alphar, loglik, lambda = moi, O = O)
})
col <- which.max(apply(complete,2,max))
row <- which.max(complete[,col])
colnames(complete)<- as.character(moir)
rownames(complete)<- as.character(alphar)
long <- melt(complete)
gnt1.eff <- alphar[row]

#gnt1
qplot(data=long, x = Var1, y = Var2, fill = value, geom="tile") + 
scale_fill_gradientn(colours = c("black","black","#000033","#000077","blue","purple","red","yellow","white"), name = "LogLik") + theme_bw() + ylab("MoI") + 
xlab("Capture efficiency") + geom_point(data = data.frame(Var2 = moir[col], Var1 = alphar[row], value = 1), shape = 3,size=2) + theme(panel.grid = element_blank())

Warning message:
“`qplot()` was deprecated in ggplot2 3.4.0.”

# gnt2
O2 <- table(apply(gnt2,2,sum))
complete <- sapply(moir, function(moi) {
  sapply(alphar, loglik, lambda = moi, O = O2)
})
col <- which.max(apply(complete,2,max))
row <- which.max(complete[,col])
colnames(complete)<- as.character(moir)
rownames(complete)<- as.character(alphar)
long <- melt(complete)
gnt2.eff <- alphar[row]
qplot(data=long, x = Var1, y = Var2, fill = value, geom="tile") + scale_fill_gradientn(colours = c("black","black","#000033","#000077","blue","purple","red","yellow","white"), name = "LogLik") + theme_bw() + ylab("MoI") + xlab("Capture efficiency") + geom_point(data = data.frame(Var2 = moir[col], Var1 = alphar[row], value = 1), shape = 3,size=2) + theme(panel.grid = element_blank())

# gn1
O2 <- table(apply(gn1,2,sum))
complete <- sapply(moir, function(moi) {
  sapply(alphar, loglik, lambda = moi, O = O2)
})
col <- which.max(apply(complete,2,max))
row <- which.max(complete[,col])
colnames(complete)<- as.character(moir)
rownames(complete)<- as.character(alphar)
long <- melt(complete)
gn1.eff <- alphar[row]
qplot(data=long, x = Var1, y = Var2, fill = value, geom="tile") + scale_fill_gradientn(colours = c("black","black","#000033","#000077","blue","purple","red","yellow","white"), name = "LogLik") + theme_bw() + ylab("MoI") + xlab("Capture efficiency") + geom_point(data = data.frame(Var2 = moir[col], Var1 = alphar[row], value = 1), shape = 3,size=2) + theme(panel.grid = element_blank())

# gn2
O2 <- table(apply(gn2,2,sum))
complete <- sapply(moir, function(moi) {
  sapply(alphar, loglik, lambda = moi, O = O2)
})
col <- which.max(apply(complete,2,max))
row <- which.max(complete[,col])
colnames(complete)<- as.character(moir)
rownames(complete)<- as.character(alphar)
long <- melt(complete)
gn2.eff <- alphar[row]
qplot(data=long, x = Var1, y = Var2, fill = value, geom="tile") + scale_fill_gradientn(colours = c("black","black","#000033","#000077","blue","purple","red","yellow","white"), name = "LogLik") + theme_bw() + ylab("MoI") + xlab("Capture efficiency") + geom_point(data = data.frame(Var2 = moir[col], Var1 = alphar[row], value = 1), shape = 3,size=2) + theme(panel.grid = element_blank())

# gr1
O2 <- table(apply(gr1,2,sum))
complete <- sapply(moir, function(moi) {
  sapply(alphar, loglik, lambda = moi, O = O2)
})
col <- which.max(apply(complete,2,max))
row <- which.max(complete[,col])
colnames(complete)<- as.character(moir)
rownames(complete)<- as.character(alphar)
long <- melt(complete)
gr1.eff <- alphar[row]
qplot(data=long, x = Var1, y = Var2, fill = value, geom="tile") + scale_fill_gradientn(colours = c("black","black","#000033","#000077","blue","purple","red","yellow","white"), name = "LogLik") + theme_bw() + ylab("MoI") + xlab("Capture efficiency") + geom_point(data = data.frame(Var2 = moir[col], Var1 = alphar[row], value = 1), shape = 3,size=2) + theme(panel.grid = element_blank())

# gr2
O2 <- table(apply(gr2,2,sum))
complete <- sapply(moir, function(moi) {
  sapply(alphar, loglik, lambda = moi, O = O2)
})
col <- which.max(apply(complete,2,max))
row <- which.max(complete[,col])
colnames(complete)<- as.character(moir)
rownames(complete)<- as.character(alphar)
long <- melt(complete)
gr2.eff <- alphar[row]
qplot(data=long, x = Var1, y = Var2, fill = value, geom="tile") + scale_fill_gradientn(colours = c("black","black","#000033","#000077","blue","purple","red","yellow","white"), name = "LogLik") + theme_bw() + ylab("MoI") + xlab("Capture efficiency") + geom_point(data = data.frame(Var2 = moir[col], Var1 = alphar[row], value = 1), shape = 3,size=2) + theme(panel.grid = element_blank())

# grt1
O2 <- table(apply(grt1,2,sum))
complete <- sapply(moir, function(moi) {
  sapply(alphar, loglik, lambda = moi, O = O2)
})
col <- which.max(apply(complete,2,max))
row <- which.max(complete[,col])
colnames(complete)<- as.character(moir)
rownames(complete)<- as.character(alphar)
long <- melt(complete)
grt1.eff <- alphar[row]
qplot(data=long, x = Var1, y = Var2, fill = value, geom="tile") + scale_fill_gradientn(colours = c("black","black","#000033","#000077","blue","purple","red","yellow","white"), name = "LogLik") + theme_bw() + ylab("MoI") + xlab("Capture efficiency") + geom_point(data = data.frame(Var2 = moir[col], Var1 = alphar[row], value = 1), shape = 3,size=2) + theme(panel.grid = element_blank())

# grt2
O2 <- table(apply(grt2,2,sum))
complete <- sapply(moir, function(moi) {
  sapply(alphar, loglik, lambda = moi, O = O2)
})
col <- which.max(apply(complete,2,max))
row <- which.max(complete[,col])
colnames(complete)<- as.character(moir)
rownames(complete)<- as.character(alphar)
long <- melt(complete)
grt2.eff <- alphar[row]
qplot(data=long, x = Var1, y = Var2, fill = value, geom="tile") + scale_fill_gradientn(colours = c("black","black","#000033","#000077","blue","purple","red","yellow","white"), name = "LogLik") + theme_bw() + ylab("MoI") + xlab("Capture efficiency") + geom_point(data = data.frame(Var2 = moir[col], Var1 = alphar[row], value = 1), shape = 3,size=2) + theme(panel.grid = element_blank())

Capture efficiency after gRNA thresholding and cell filtering (raw vs SCTnormalized)

bardata <- data.frame(method = c("Raw_1_Threshold_Run1", "Raw_1_Threshold_Run2", "Raw_2_Threshold_Run1", "Raw_2_Threshold_Run2", "Normalized_1_Threshold_Run1", "Normalized_1_Threshold_Run2",  "Normalized_2_Threshold_Run1", "Normalized_2_Threshold_Run2"), eff = c(gr1.eff, gr2.eff, grt1.eff, grt2.eff, gn1.eff, gn2.eff, gnt1.eff, gnt2.eff))
qplot(x = reorder(method,eff), y = eff, data= bardata,fill=method, geom="col") + 
scale_fill_manual(guide=F, name = "Method", values =c("Raw_1_Threshold_Run1" = "#666666", "Raw_1_Threshold_Run2" = "#666666", "Raw_2_Threshold_Run1" = "#666666", "Raw_2_Threshold_Run2" = "#666666", "Normalized_1_Threshold_Run1" = "#666666", "Normalized_1_Threshold_Run2" = "#666666", "Normalized_2_Threshold_Run1" = "#666666", "Normalized_2_Threshold_Run2" = "#666666")) + 
theme_bw() + theme(panel.grid = element_blank(),panel.border = element_rect(fill = NA, size=1), axis.text.y = element_text(colour = "black"), axis.text.x = element_text(angle=60, colour="black", hjust=1)) + xlab("") + ylab("gRNA capture efficiency") + scale_y_continuous(breaks = seq(0,1,by=0.25), limits = c(0,1))

Warning message:
“The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.”
Warning message:
“The `guide` argument in `scale_*()` cannot be `FALSE`. This was deprecated in ggplot2 3.3.4.
ℹ Please use "none" instead.”

bardata <- data.frame(method = c("Before Filtering Run1", "Before Filtering Run2",  "After Filtering Run1", "After Filtering Run2"), eff = c(gn1.eff, gn2.eff, gnt1.eff, gnt2.eff))
qplot(x = reorder(method,eff), y = eff, data= bardata,fill=method, geom="col") + 
scale_fill_manual(guide=F, name = "Method", values =c("Before Filtering Run1" = "#666666", "Before Filtering Run2" = "#666666", "After Filtering Run1" = "#666666", "After Filtering Run2" = "#666666")) + 
theme_bw() + xlab("") + ylab("gRNA capture efficiency") + theme(panel.grid = element_blank(),panel.border = element_rect(fill = NA, size=1), axis.text.y = element_text(colour = "black", size=16), axis.text.x = element_text( colour="black",size=16), axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + scale_y_continuous(breaks = seq(0,1,by=0.25), limits = c(0,1))+ coord_flip()

pdf("gRNA_capture_efficiency_before_after_filtering_202212.pdf",width=6,height=6)
bardata <- data.frame(method = c("Before Filtering Run1", "Before Filtering Run2",  "After Filtering Run1", "After Filtering Run2"), eff = c(gn1.eff, gn2.eff, gnt1.eff, gnt2.eff))
qplot(x = reorder(method,eff), y = eff, data= bardata,fill=method, geom="col") + 
scale_fill_manual(guide=F, name = "Method", values =c("Before Filtering Run1" = "#666666", "Before Filtering Run2" = "#666666", "After Filtering Run1" = "#666666", "After Filtering Run2" = "#666666")) + 
theme_bw() + xlab("") + ylab("gRNA capture efficiency") + theme(panel.grid = element_blank(),panel.border = element_rect(fill = NA, size=1), axis.text.y = element_text(colour = "black", size=16), axis.text.x = element_text( colour="black",size=16), axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + scale_y_continuous(breaks = seq(0,1,by=0.25), limits = c(0,1))+ coord_flip()
dev.off()

png: 2

pdf("gRNA_capture_efficiency_202212.pdf",width=6,height=6)
qplot(x = reorder(method,eff), y = eff, data= bardata,fill=method, geom="col") + 
scale_fill_manual(guide=F, name = "Method", values =c("Raw_1_Threshold_Run1" = "#666666", "Raw_1_Threshold_Run2" = "#666666", "Raw_2_Threshold_Run1" = "#666666", "Raw_2_Threshold_Run2" = "#666666", "Normalized_1_Threshold_Run1" = "#666666", "Normalized_1_Threshold_Run2" = "#666666", "Normalized_2_Threshold_Run1" = "#666666", "Normalized_2_Threshold_Run2" = "#666666")) + 
theme_bw() + theme(panel.grid = element_blank(),panel.border = element_rect(fill = NA, size=1), axis.text.y = element_text(colour = "black"), axis.text.x = element_text(angle=60, colour="black", hjust=1)) + xlab("") + ylab("gRNA capture efficiency") + scale_y_continuous(breaks = seq(0,1,by=0.25), limits = c(0,1))
dev.off()

png: 2

cat("Raw_1_Threshold_Run1")
gr1.eff
cat("Raw_1_Threshold_Run2")
gr2.eff
cat("Raw_2_Threshold_Run1")
grt1.eff
cat("Raw_2_Threshold_Run2")
grt2.eff
cat("Normalized_1_Threshold_Run1")
gn1.eff
cat("Normalized_1_Threshold_Run2")
gn2.eff
cat("Normalized_2_Threshold_Run1")
gnt1.eff
cat("Normalized_2_Threshold_Run2")
gnt2.eff

Raw_1_Threshold_Run1

1

Raw_1_Threshold_Run2

1

Raw_2_Threshold_Run1

1

Raw_2_Threshold_Run2

1

Normalized_1_Threshold_Run1

0.998

Normalized_1_Threshold_Run2

0.998

Normalized_2_Threshold_Run1

0.998

Normalized_2_Threshold_Run2

0.998

# Nr cells
# Capture rate
length(colnames(t1)[which(apply(gr1,2,sum) != 0)])
length(colnames(t2)[which(apply(gr2,2,sum) != 0)])
length(colnames(t1)[which(apply(grt1,2,sum) != 0)])
length(colnames(t2)[which(apply(grt2,2,sum) != 0)])
length(colnames(t1)[which(apply(gn1,2,sum) != 0)])
length(colnames(t2)[which(apply(gn2,2,sum) != 0)])
length(colnames(t1)[which(apply(gnt1,2,sum) != 0)])
length(colnames(t2)[which(apply(gnt2,2,sum) != 0)])

6196

10363

6196

10363

6188

10347

6188

10347

# Capture rate
length(colnames(t1)[which(apply(gr1,2,sum) != 0)])/12597
length(colnames(t2)[which(apply(gr2,2,sum) != 0)])/19406
length(colnames(t1)[which(apply(grt1,2,sum) != 0)])/12597
length(colnames(t2)[which(apply(grt2,2,sum) != 0)])/19406
length(colnames(t1)[which(apply(gn1,2,sum) != 0)])/12597
length(colnames(t2)[which(apply(gn2,2,sum) != 0)])/19406
length(colnames(t1)[which(apply(gnt1,2,sum) != 0)])/12597
length(colnames(t2)[which(apply(gnt2,2,sum) != 0)])/19406

0.491863142017941

0.534010099969082

0.491863142017941

0.534010099969082

0.491228070175439

0.533185612697104

0.491228070175439

0.533185612697104

# Number of control cells
sum(grc1)
sum(grc2)
sum(grtc1)
sum(grtc2)
sum(gnc1)
sum(gnc2)
sum(gntc1)
sum(gntc2)

206

370

206

370

206

370

206

370

gRNA threshold (bacth-corrected counts > 1)

gRNA_scheme1 <- gnt1[-sort(match(control_idx,rownames(gnt1))),]
gRNA_scheme1[gRNA_scheme1==1]="perturbed"
gRNA_scheme1[,gntc1] = "control"
gRNA_scheme1[gRNA_scheme1==0] = "perturbed_by_others"
t1@meta.data <- cbind(t1@meta.data, as.data.frame(t(gRNA_scheme1)))
gRNA_scheme2 <- gnt2[-sort(match(control_idx,rownames(gnt2))),]
gRNA_scheme2[gRNA_scheme2==1]="perturbed"
gRNA_scheme2[,gntc2] = "control"
gRNA_scheme2[gRNA_scheme2==0] = "perturbed_by_others"
t2@meta.data <- cbind(t2@meta.data, as.data.frame(t(gRNA_scheme2)))

br_anno <- read.table("../../Dusa/new_rhapsody_regions_bins_guides_results.txt", sep="\t", header=TRUE)
br_anno <- br_anno[which((br_anno$class != "NEG-CONTROL") & (br_anno$class != "non-targctrl")),]
br_anno <- br_anno[!is.na(match(br_anno$Rhapsody_name, colnames(t1@meta.data))),]
#bin1 <- c()
#for (i in names(table(br_anno$Bin))){
#    if(length(br_anno$Rhapsody_name[which(br_anno$Bin==i)])==1){
#        dat <- t1@meta.data[,br_anno$Rhapsody_name[which(br_anno$Bin==i)]]
#    } else {
#        dat <- rowSums(t1@meta.data[,br_anno$Rhapsody_name[which(br_anno$Bin==i)]]=="perturbed")
#        dat[which(dat>=1)]="perturbed"
#        dat[which(rowSums(t1@meta.data[,br_anno$Rhapsody_name[which(br_anno$Bin==i)]]=="control")>0)]="control"
#        dat[which(dat=='0')]="perturbed_by_others"
#    }
#    bin1 <- cbind(bin1,dat)
#} 
#colnames(bin1) <- names(table(br_anno$Bin))
reg1 <- c()
for (i in names(table(br_anno$Region_name))){
    if(length(br_anno$Rhapsody_name[which(br_anno$Region_name==i)])==1){
        dat <- t1@meta.data[,br_anno$Rhapsody_name[which(br_anno$Region_name==i)]]
    } else {
        dat <- rowSums(t1@meta.data[,br_anno$Rhapsody_name[which(br_anno$Region_name==i)]]=="perturbed")
        dat[which(dat>=1)]="perturbed"
        dat[which(rowSums(t1@meta.data[,br_anno$Rhapsody_name[which(br_anno$Region_name==i)]]=="control")>0)]="control"
        dat[which(dat=='0')]="perturbed_by_others"
    }
    reg1 <- cbind(reg1,dat)
} 
colnames(reg1) <- names(table(br_anno$Region_name))
#t1@meta.data <- cbind(t1@meta.data,bin1)
t1@meta.data <- cbind(t1@meta.data,reg1)

br_anno <- read.table("../../Dusa/new_rhapsody_regions_bins_guides_results.txt", sep="\t", header=TRUE)
br_anno <- br_anno[which((br_anno$class != "NEG-CONTROL") & (br_anno$class != "non-targctrl")),]
br_anno <- br_anno[!is.na(match(br_anno$Rhapsody_name, colnames(t2@meta.data))),]
#bin2 <- c()
#for (i in names(table(br_anno$Bin))){
#    if(length(br_anno$Rhapsody_name[which(br_anno$Bin==i)])==1){
#        dat <- t2@meta.data[,br_anno$Rhapsody_name[which(br_anno$Bin==i)]]
#    } else {
#        dat <- rowSums(t2@meta.data[,br_anno$Rhapsody_name[which(br_anno$Bin==i)]]=="perturbed")
#        dat[which(dat>=1)]="perturbed"
#        dat[which(rowSums(t2@meta.data[,br_anno$Rhapsody_name[which(br_anno$Bin==i)]]=="control")>0)]="control"
#        dat[which(dat=='0')]="perturbed_by_others"
#    }
#    bin2 <- cbind(bin2,dat)
#} 
#colnames(bin2) <- names(table(br_anno$Bin))
reg2 <- c()
for (i in names(table(br_anno$Region_name))){
    if(length(br_anno$Rhapsody_name[which(br_anno$Region_name==i)])==1){
        dat <- t2@meta.data[,br_anno$Rhapsody_name[which(br_anno$Region_name==i)]]
    } else {
        dat <- rowSums(t2@meta.data[,br_anno$Rhapsody_name[which(br_anno$Region_name==i)]]=="perturbed")
        dat[which(dat>=1)]="perturbed"
        dat[which(rowSums(t2@meta.data[,br_anno$Rhapsody_name[which(br_anno$Region_name==i)]]=="control")>0)]="control"
        dat[which(dat=='0')]="perturbed_by_others"
    }
    reg2 <- cbind(reg2,dat)
} 
colnames(reg2) <- names(table(br_anno$Region_name))
#t2@meta.data <- cbind(t2@meta.data,bin2)
t2@meta.data <- cbind(t2@meta.data,reg2)

Filter cells that don't contain any gRNA

t1 <- subset(t1, cells=colnames(t1)[which(apply(gnt1,2,sum) != 0)])
g1 <- subset(g1, cells=colnames(g1)[which(apply(gnt1,2,sum) != 0)])
t2 <- subset(t2, cells=colnames(t2)[which(apply(gnt2,2,sum) != 0)])
g2 <- subset(g2, cells=colnames(g2)[which(apply(gnt2,2,sum) != 0)])
save(t1,g1, file = "../../Dusa/Run1_filtered_2.rdata")
save(t2,g2, file = "../../Dusa/Run2_filtered_2.rdata")

load("../../Dusa/Run1_filtered_2.rdata")
load("../../Dusa/Run2_filtered_2.rdata")

t1

An object of class Seurat 
125 features across 6188 samples within 2 assays 
Active assay: SCT (59 features, 59 variable features)
 1 other assay present: RNA

g1

An object of class Seurat 
2183 features across 6188 samples within 2 assays 
Active assay: SCT (1086 features, 1086 variable features)
 1 other assay present: RNA

t2

An object of class Seurat 
125 features across 10347 samples within 2 assays 
Active assay: SCT (59 features, 59 variable features)
 1 other assay present: RNA

g2

An object of class Seurat 
2183 features across 10347 samples within 2 assays 
Active assay: SCT (1086 features, 1086 variable features)
 1 other assay present: RNA

summary(colSums(t1@assays$SCT@data))
summary(colSums(t2@assays$SCT@data))

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  12.14   28.59   31.86   31.95   35.26   53.38 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  15.71   30.15   33.20   33.53   36.64   52.81 

summary(colSums(g1@assays$SCT@data))
summary(colSums(g2@assays$SCT@data))

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  2.996   4.787   5.215   5.709   5.666  20.472 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  2.303   4.111   4.564   5.078   5.088  20.044 

Comt <- merge(t1, y = t2, add.cell.ids = c("R1", "R2"), project = "Rhapsody")

Comt <- SCTransform(Comt, vars.to.regress = "orig.ident")

Calculating cell attributes from input UMI matrix: log_umi

Variance stabilizing transformation of count matrix of size 59 by 16535

Model formula is y ~ log_umi

Get Negative Binomial regression parameters per gene

Using 56 genes, 5000 cells

  |======================================================================| 100%

Second step: Get residuals using fitted parameters for 59 genes

  |======================================================================| 100%

Computing corrected count matrix for 59 genes

  |======================================================================| 100%

Calculating gene attributes

Wall clock passed: Time difference of 5.218403 secs

Determine variable features

Place corrected count matrix in counts slot

Regressing out orig.ident

Centering data matrix

Set default assay to SCT

Comt

An object of class Seurat 
125 features across 16535 samples within 2 assays 
Active assay: SCT (59 features, 59 variable features)
 1 other assay present: RNA

Comt@meta.data[is.na(Comt@meta.data)] <- "perturbed_by_others"

saveRDS(Comt, file = "./Rhapsody_BC.rds")

rc.integrated <- readRDS("./Rhapsody_BC.rds")

df <- data.frame(RNA_count=colSums(rc.integrated@assays$RNA@counts), Run=rc.integrated$orig.ident)
ggplot(df, aes(x=RNA_count, color=Run)) +
  geom_histogram(fill="white", alpha=0.5, position="identity", bins=60)+theme_classic()+xlab("RNA raw counts (UMI)")+ylab("Cell count")+ggtitle("Gene UMI/cell")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))

df <- data.frame(RNA_count=colSums(rc.integrated@assays$SCT@data), Run=rc.integrated$orig.ident)
ggplot(df, aes(x=RNA_count, color=Run)) +
  geom_histogram(fill="white", alpha=0.5, position="identity", bins=60)+theme_classic()+xlab("log1p(SCT normalized counts)")+ylab("Cell count")+ggtitle("Batch-corrected normalized gene UMI/cell")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))

Two runs vs integration

gint <- column_to_rownames(full_join(rownames_to_column(as.data.frame(g1@assays$SCT@data),var = "rownames"), rownames_to_column(as.data.frame(g2@assays$SCT@data),var="rownames"), by="rownames"), var = "rownames")
gint[is.na(gint)] <- 0

dat <- data.frame(treatment=rep("Run1", length(apply(g1@assays$SCT@data>1,1,sum))), nrcell_per_gRNA=apply(g1@assays$SCT@data>1,1,sum))
dat <- rbind(dat, data.frame(treatment=rep("Run2", length(apply(g2@assays$SCT@data>1,1,sum))), nrcell_per_gRNA=apply(g2@assays$SCT@data>1,1,sum)))
dat <- rbind(dat, data.frame(treatment=rep("Integrated", length(apply(gint>1,1,sum))), nrcell_per_gRNA=apply(gint>1,1,sum)))

dat <- within(dat, treatment <- factor(treatment, levels= c("Run1","Run2","Integrated")))

options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, nrcell_per_gRNA)) + geom_boxplot(outlier.shape=NA) + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme_classic()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

pdf("nrcell_per_gRNA_2counts_1_202212.pdf",width=6,height=6)
ggplot(dat, aes(treatment, nrcell_per_gRNA)) + geom_boxplot(outlier.shape=NA) + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+ 
  theme_classic()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()

png: 2

options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, nrcell_per_gRNA)) + geom_boxplot(outlier.shape=NA) + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20)) + coord_cartesian(ylim = c(0, 90))

pdf("nrcell_per_gRNA_2counts_2_202212.pdf",width=6,height=6)
ggplot(dat, aes(treatment, nrcell_per_gRNA)) + geom_boxplot(outlier.shape=NA) + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20)) + coord_cartesian(ylim = c(0, 90))
dev.off()

png: 2

## gRNA summary
cat("Run1")
summary(apply(g1@assays$SCT@data>1,1,sum))
cat("Run2")
summary(apply(g2@assays$SCT@data>1,1,sum))
cat("Integrated")
summary(apply(gint>1,1,sum))

Run1

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   4.000   6.000   6.608   9.000  22.000 

Run2

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   2.00    8.00   11.00   11.43   14.00   38.00 

Integrated

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   5.00   13.00   17.00   18.03   22.00   58.00 

## Region summary
rint <- column_to_rownames(full_join(rownames_to_column(as.data.frame(t(reg1)),var = "rownames"), rownames_to_column(as.data.frame(t(reg2)),var="rownames"), by="rownames"), var = "rownames")
rint[is.na(rint)] <- 0

dat <- data.frame(treatment=rep("Run1", length(apply(reg1=="perturbed",2,sum))), nrcell_per_region=apply(reg1=="perturbed",2,sum))
dat <- rbind(dat, data.frame(treatment=rep("Run2", length(apply(reg2=="perturbed",2,sum))), nrcell_per_region=apply(reg2=="perturbed",2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("Integrated", length(apply(rint=="perturbed",1,sum))), nrcell_per_region=apply(rint=="perturbed",1,sum)))
dat <- within(dat, treatment <- factor(treatment, levels= c("Run1","Run2","Integrated")))

options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, nrcell_per_region)) + geom_boxplot(outlier.shape=NA) + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20)) + coord_cartesian(ylim = c(0, 200))

pdf("nrcell_per_region_2counts_1_202212.pdf",width=6,height=6)
ggplot(dat, aes(treatment, nrcell_per_region)) + geom_boxplot(outlier.shape=NA) + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20)) + coord_cartesian(ylim = c(0, 200))
dev.off()

png: 2

dat <- data.frame(treatment=rep("gRNA", length(apply(gint>1,1,sum))), nrcell=apply(gint>1,1,sum))
#dat <- rbind(dat, data.frame(treatment=rep("bin", length(apply(bint=="perturbed",1,sum))), nrcell=apply(bint=="perturbed",1,sum)))
dat <- rbind(dat, data.frame(treatment=rep("region", length(apply(rint=="perturbed",1,sum))), nrcell=apply(rint=="perturbed",1,sum)))
dat <- within(dat, treatment <- factor(treatment, levels= c("gRNA","bin","region")))

options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, nrcell)) + geom_boxplot(outlier.shape=NA) + theme_minimal() + ylab("number of cells per gRNA/region") + 
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20)) + coord_cartesian(ylim = c(0, 200))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, nrcell)) + geom_boxplot(outlier.shape=NA) + theme_minimal() + ylab("number of cells per gRNA/region") + 
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20)) +
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

dat %>% filter(treatment=='gRNA') %>% summary()

  treatment        nrcell     
 gRNA  :1086   Min.   : 5.00  
 bin   :   0   1st Qu.:13.00  
 region:   0   Median :17.00  
               Mean   :18.03  
               3rd Qu.:22.00  
               Max.   :58.00  

dat %>% filter(treatment=='region') %>% summary()

  treatment       nrcell      
 gRNA  :  0   Min.   :  9.00  
 bin   :  0   1st Qu.: 42.25  
 region:222   Median : 68.00  
              Mean   : 81.39  
              3rd Qu.: 96.25  
              Max.   :597.00  

pdf("nrcell_per_gRNA_region_202212.pdf",width=6,height=6)
ggplot(dat, aes(treatment, nrcell)) + geom_boxplot(outlier.shape=NA) + theme_minimal() + ylab("number of cells per gRNA/bin/region") + 
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20)) + coord_cartesian(ylim = c(0, 200))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()

png: 2

cat("Run1")
summary(apply(reg1=="perturbed",2,sum))
cat("Run2")
summary(apply(reg2=="perturbed",2,sum))
cat("Integrated")
summary(apply(rint=="perturbed",1,sum))

Run1

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   1.00   16.00   24.00   30.01   36.00  236.00 

Run2

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   6.00   25.25   43.00   51.38   60.00  374.00 

Integrated

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   9.00   42.25   68.00   81.39   96.25  597.00 

dat <- data.frame(treatment=rep("Run1", length(apply(g1@assays$SCT@data>1,2,sum))), gRNA_per_cell=apply(g1@assays$SCT@data>1,2,sum))
dat <- rbind(dat, data.frame(treatment=rep("Run2", length(apply(g2@assays$SCT@data>1,2,sum))), gRNA_per_cell=apply(g2@assays$SCT@data>1,2,sum)))
dat <- rbind(dat, data.frame(treatment=rep("Integrated", length(apply(gint>1,2,sum))), gRNA_per_cell=apply(gint>1,2,sum)))
dat <- within(dat, treatment <- factor(treatment, levels= c("Run1","Run2","Integrated")))

options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, gRNA_per_cell)) + geom_boxplot(outlier.shape=NA) + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

pdf("gRNA_per_cell_2counts_3_202212.pdf",width=6,height=6)
ggplot(dat, aes(treatment, gRNA_per_cell)) + geom_boxplot(outlier.shape=NA) + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()

png: 2

options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, gRNA_per_cell)) + geom_boxplot(outlier.shape=NA) + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20)) + coord_cartesian(ylim = c(0, 5))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

pdf("gRNA_per_cell_2counts_4_202212.pdf",width=6,height=6)
ggplot(dat, aes(treatment, gRNA_per_cell)) + geom_boxplot(outlier.shape=NA) + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20)) + coord_cartesian(ylim = c(0, 5))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()

png: 2

cat("Run1")
summary(apply(g1@assays$SCT@data>1,2,sum))
cat("Run2")
summary(apply(g2@assays$SCT@data>1,2,sum))
cat("Integrated")
summary(apply(gint>1,2,sum))

Run1

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   1.00    1.00    1.00    1.16    1.00    4.00 

Run2

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  1.000   1.000   1.000   1.199   1.000   4.000 

Integrated

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  1.000   1.000   1.000   1.184   1.000   4.000 

Prepare for DE

#For each cell, how many of the genes were detected on average? A: 17
mean(apply(rc.integrated@assays$SCT@data,2,function(x){sum(x>0)}))

17.0035681886907

rc.integrated@meta.data <- rc.integrated@meta.data[,-grep("^PHOX2B|^Region",colnames(rc.integrated@meta.data))]

br_anno <- read.table("../../Dusa/new_rhapsody_regions_bins_guides_results.txt", sep="\t", header=TRUE)
br_anno <- br_anno[which((br_anno$class != "NEG-CONTROL") & (br_anno$class != "non-targctrl")),]
br_anno <- br_anno[!is.na(match(br_anno$Rhapsody_name, colnames(rc.integrated@meta.data))),]
# Set all "perturbed_by_others" to "control" 
for (i in grep("^X",colnames(rc.integrated@meta.data))){
    rc.integrated@meta.data[,i] <- gsub("perturbed_by_others", "control", rc.integrated@meta.data[,i], ignore.case = FALSE, perl = FALSE,fixed = T, useBytes = FALSE)
}
# Set "control"s within same Region or +/- 400 kb distance region to "perturbed_by_others" 
for (i in 1:length(grep("^X",colnames(rc.integrated@meta.data)))){
    idx <- colnames(rc.integrated@meta.data[,grep("^X",colnames(rc.integrated@meta.data))][i])
    tidx <- which(br_anno$Rhapsody_name==colnames(rc.integrated@meta.data[,grep("^X",colnames(rc.integrated@meta.data))][i]))
    hidx <- br_anno$Rhapsody_name[which(br_anno$guide_start > (br_anno$guide_start[tidx]-400000) & br_anno$guide_start < (br_anno$guide_end[tidx]+400000) & br_anno$guide_end > (br_anno$guide_start[tidx]-400000) & br_anno$guide_end < (br_anno$guide_end[tidx]+400000))]
    kidx <- br_anno$Rhapsody_name[which(br_anno$Region_name==br_anno$Region_name[tidx])]
    ridx <- unique(hidx, kidx)
    
    if (length(ridx)>2){
        rc.integrated@meta.data[which(apply(rc.integrated@meta.data[,ridx[which(ridx != idx)]],1, function(x)sum(x=="perturbed"))>=1),idx]="perturbed_by_others"
    } else if (length(ridx)>1) {
        rc.integrated@meta.data[which(rc.integrated@meta.data[,ridx[which(ridx != idx)]]=="perturbed"),idx]="perturbed_by_others"
    }
}

#bin <- c()
#for (i in names(table(br_anno$Bin))){
#    if(length(br_anno$Rhapsody_name[which(br_anno$Bin==i)])==1){
#        dat <- rc.integrated@meta.data[,br_anno$Rhapsody_name[which(br_anno$Bin==i)]]
#    } else {
#        dat <- rowSums(rc.integrated@meta.data[,br_anno$Rhapsody_name[which(br_anno$Bin==i)]]=="perturbed")
#        dat[which(dat>=1)]="perturbed"
#        dat[which(rowSums(rc.integrated@meta.data[,br_anno$Rhapsody_name[which(br_anno$Bin==i)]]=="perturbed_by_others")>=1 & dat!="perturbed")]="perturbed_by_others"
#        dat[which(dat=='0')]="control"
#    }
#    bin <- cbind(bin,dat)
#} 
#colnames(bin) <- names(table(br_anno$Bin))
reg <- c()
for (i in names(table(br_anno$Region_name))){
    if(length(br_anno$Rhapsody_name[which(br_anno$Region_name==i)])==1){
        dat <- rc.integrated@meta.data[,br_anno$Rhapsody_name[which(br_anno$Region_name==i)]]
    } else {
        dat <- rowSums(rc.integrated@meta.data[,br_anno$Rhapsody_name[which(br_anno$Region_name==i)]]=="perturbed")
        dat[which(dat>=1)]="perturbed"
        dat[which(rowSums(rc.integrated@meta.data[,br_anno$Rhapsody_name[which(br_anno$Region_name==i)]]=="perturbed_by_others")>=1 & dat!="perturbed")]="perturbed_by_others"
        dat[which(dat=='0')]="control"
    }
    reg <- cbind(reg,dat)
} 
colnames(reg) <- names(table(br_anno$Region_name))

#rc.integrated@meta.data <- cbind(rc.integrated@meta.data,bin)
rc.integrated@meta.data <- cbind(rc.integrated@meta.data,reg)

TAP.nods <- as.matrix(rc.integrated@assays$SCT@data)
ngenes <- apply(TAP.nods > 0 , 2, sum)

hist(ngenes)

save(rc.integrated, ngenes, file = "../../Dusa/Rhapsody_MAST_input.rdata")

load(file = "../../Dusa/Rhapsody_MAST_input.rdata")

Plot gene expression level (SCT)

gene_name <- "PHOX2B"

pos_idx <- as.numeric(which(apply(rc.integrated@meta.data[pr_anno$name[which(pr_anno$prom_name==gene_name)]],1, function(x) sum(which(x=="perturbed")))>=1))
pt <- rep("No", ncol(rc.integrated))
pt[pos_idx] <- "Yes"   
dat <- data.frame(expression_level = rc.integrated@assays$SCT@data[gene_name,], promoter_targeted = pt)
wilcox.test(dat$expression_level[which(dat$promoter_targeted=="No")], dat$expression_level[which(dat$promoter_targeted=="Yes")])                                  
ggplot(dat, aes(x=promoter_targeted, y=expression_level, color=promoter_targeted)) + 
  geom_boxplot(outlier.shape=NA)+theme_minimal() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))
#+coord_cartesian(ylim = c(0, 60))

	Wilcoxon rank sum test with continuity correction

data:  dat$expression_level[which(dat$promoter_targeted == "No")] and dat$expression_level[which(dat$promoter_targeted == "Yes")]
W = 988327, p-value = 1.146e-09
alternative hypothesis: true location shift is not equal to 0

pdf("PHOX2B_expr_sct_202212.pdf",width=4,height=6)
ggplot(dat, aes(x=promoter_targeted, y=expression_level, color=promoter_targeted)) + 
  geom_boxplot()+theme_minimal() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))
dev.off()

png: 2

gene_name <- "SHISA3"

pos_idx <- as.numeric(which(apply(rc.integrated@meta.data[pr_anno$name[which(pr_anno$prom_name==gene_name)]],1, function(x) sum(which(x=="perturbed")))>=1))
pt <- rep("No", ncol(rc.integrated))
pt[pos_idx] <- "Yes"   
dat <- data.frame(expression_level = rc.integrated@assays$SCT@data[gene_name,], promoter_targeted = pt)
wilcox.test(dat$expression_level[which(dat$promoter_targeted=="No")], dat$expression_level[which(dat$promoter_targeted=="Yes")])
ggplot(dat, aes(x=promoter_targeted, y=expression_level, color=promoter_targeted)) + 
  geom_boxplot(outlier.shape=NA)+ theme_minimal() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))
                                 # + coord_cartesian(ylim = c(0, 25))

	Wilcoxon rank sum test with continuity correction

data:  dat$expression_level[which(dat$promoter_targeted == "No")] and dat$expression_level[which(dat$promoter_targeted == "Yes")]
W = 462772, p-value < 2.2e-16
alternative hypothesis: true location shift is not equal to 0

pdf("SHISA3_expr_sct_202212.pdf",width=4,height=6)
ggplot(dat, aes(x=promoter_targeted, y=expression_level, color=promoter_targeted)) + 
  geom_boxplot(outlier.shape=NA)+ theme_minimal() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))
dev.off()

png: 2

gene_name <- "BEND4"

pos_idx <- as.numeric(which(apply(rc.integrated@meta.data[pr_anno$name[which(pr_anno$prom_name==gene_name)]],1, function(x) sum(which(x=="perturbed")))>=1))
pt <- rep("No", ncol(rc.integrated))
pt[pos_idx] <- "Yes"   
dat <- data.frame(expression_level = rc.integrated@assays$SCT@data[gene_name,], promoter_targeted = pt)
wilcox.test(dat$expression_level[which(dat$promoter_targeted=="No")], dat$expression_level[which(dat$promoter_targeted=="Yes")])
ggplot(dat, aes(x=promoter_targeted, y=expression_level, color=promoter_targeted)) + geom_boxplot(outlier.shape=NA)+ theme_minimal() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))
                                  #+ coord_cartesian(ylim = c(0, 10))

	Wilcoxon rank sum test with continuity correction

data:  dat$expression_level[which(dat$promoter_targeted == "No")] and dat$expression_level[which(dat$promoter_targeted == "Yes")]
W = 376932, p-value < 2.2e-16
alternative hypothesis: true location shift is not equal to 0

pdf("BEND4_expr_202212.pdf",width=4,height=6)
ggplot(dat, aes(x=promoter_targeted, y=expression_level, color=promoter_targeted)) + geom_boxplot(outlier.shape=NA)+ theme_minimal() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))
dev.off()

png: 2

Differential Expression Analysis

TAP_DE <- c()

Run Suerat Test (gRNA)

gRNA_scheme <- t(as.matrix(rc.integrated@meta.data[,grep("^X", colnames(rc.integrated@meta.data))]))

table(gRNA_scheme[1,])

            control           perturbed perturbed_by_others 
              13350                  22                3163 

apply(gRNA_scheme,1,table)

A matrix: 3 × 1034 of type int

	X1	X10	X100	X1000	X1001	X1002	X1003	X1004	X1005	X1006	⋯	X993	X994	X995	X996	X997	X998	X999	X1030	X248	X585
control	13350	12915	11444	11137	11346	11385	11399	9721	9437	8330	⋯	12664	11918	11722	11590	11590	11590	11246	9765	6684	8041
perturbed	22	7	16	10	9	6	24	22	13	11	⋯	20	12	22	17	14	11	23	5	6	8
perturbed_by_others	3163	3613	5075	5388	5180	5144	5112	6792	7085	8194	⋯	3851	4605	4791	4928	4931	4934	5266	6765	9845	8486

MAST cov

de_MAST <- function(pert_object) {
  
  # add some row- and colData expected by MAST (not used in DE tests)
  rowData(pert_object) <- cbind(rowData(pert_object), primerid = rownames(pert_object))
  colData(pert_object) <- cbind(colData(pert_object), wellKey = colnames(pert_object))

  # coerce pert_object to SingleCellAssay, since MAST requires that as input
  sca <- SceToSingleCellAssay(pert_object)
  
  # prepare colData for model fitting
  colnames(colData(sca))[1] <- "pert"  # make sure 1st column is called pert for coeff testing
  pert <- as.factor(colData(sca)$pert)
  levels(pert) <- c(0, 1)
  colData(sca)$pert <- pert

  # fit hurdle model
  vars <- colnames(colData(sca))
  vars_to_test <- vars[vars != "wellKey"]
  model <- paste0("~", paste(vars_to_test, collapse = "+"))
  zlm_fit <- zlm(as.formula(model), sca)
  # get logFC change for the perturbation coefficient
  summary_zlm_fit <- summary(zlm_fit, logFC = TRUE)
  summary_dt <- summary_zlm_fit$datatable
  logFC <- summary_dt[contrast == "pert1" & component == "logFC", .(primerid, coef, ci.hi, ci.lo)]

  # perform likelihood ratio test for the perturbation coefficient
  lrt <- as.data.frame(lrTest(zlm_fit, CoefficientHypothesis("pert1")))
  lrt_output <- data.frame(primerid = rownames(lrt), pvalue = lrt[, "hurdle.Pr(>Chisq)"],
                           row.names = rownames(lrt), stringsAsFactors = FALSE)
 
  # assemble and return output
  output <- merge(as.data.frame(logFC), lrt_output, by = "primerid")
  colnames(output) <- c("gene", "logFC", "ci_high", "ci_low", "pvalue")
  output[order(output$pvalue), ]
  
}

## Use SCT assay data slot
runSeuratTest <- function(g = "X1", object=rc.integrated, covariate=ngenes) { 
  
  Idents(object) <- g
  object$covariate <- covariate
  a <- colnames(object)[Idents(object) == "perturbed"]
  b <- colnames(object)[Idents(object) == "control"]

  use.a <- a
  use.b <- b
  testobject <- subset(object, cells = c(use.a, use.b))
 
  a.obj <- subset(object, cells = use.a)
  b.obj <- subset(object, cells = use.b)

  sce <- SingleCellExperiment(list(counts = GetAssayData(testobject, assay = "SCT", slot = "data"), logcounts = GetAssayData(testobject, assay = "SCT", slot = "data")) , colData = data.frame(row.names = colnames(testobject), ident = Idents(testobject), cov = testobject$covariate))
 
  MAST.result <- de_MAST(sce)

  m <- data.frame(row.names =MAST.result$gene, p_val = MAST.result$pvalue, avg_logFC = MAST.result$logFC, pct.1="NA", pct.2="NA", p_val_adj = p.adjust( MAST.result$pvalue, method = "fdr"))
    
  m$gene <- rownames(m) 
  m$ident <- g
  m$method <- "MAST.cov"
  m$ncells <- length(a)
  m
}

output <- lapply(rownames(gRNA_scheme), runSeuratTest, object = rc.integrated, covariate = ngenes)
output <- do.call(rbind, output)

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Done!

Combining coefficients and standard errors

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Done!

Combining coefficients and standard errors

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Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures


 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)


 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

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 Completed [============>-------------------------------]  29% with 0 failures

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 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

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 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

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 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

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 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

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 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

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 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

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 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

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 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

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 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

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 Completed [====================>-----------------------]  47% with 0 failures

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 Completed [=====================>----------------------]  51% with 0 failures

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 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

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 Completed [======================================>-----]  88% with 0 failures

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 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

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 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

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 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

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 Completed [=================================>----------]  78% with 0 failures

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 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

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 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

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 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)


 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

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 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)


 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures
 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

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 Completed [=======>------------------------------------]  19% with 0 failures

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 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

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 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

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 Completed [=======>------------------------------------]  19% with 0 failures

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 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [>-------------------------------------------]   3% with 0 failures

 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

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 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

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 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)


 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

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 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

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 Completed [=====================>----------------------]  51% with 0 failures

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 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

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 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

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 Completed [========================================>---]  93% with 0 failures

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 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

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 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

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 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

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 Completed [=========>----------------------------------]  24% with 0 failures

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 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

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 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

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 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

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 Completed [=======================================>----]  92% with 0 failures

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 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

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 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

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 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

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 Completed [===================>------------------------]  46% with 0 failures

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 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

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 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

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 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

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 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)


 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

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 Completed [=======>------------------------------------]  19% with 0 failures

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 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.

Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)


 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures
 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [=>------------------------------------------]   5% with 0 failures

 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Assuming data assay in position 2, with name logcounts is log-transformed.


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

 Completed [=============>------------------------------]  32% with 0 failures

 Completed [==============>-----------------------------]  34% with 0 failures

 Completed [===============>----------------------------]  36% with 0 failures

 Completed [===============>----------------------------]  37% with 0 failures

 Completed [================>---------------------------]  39% with 0 failures

 Completed [=================>--------------------------]  41% with 0 failures

 Completed [==================>-------------------------]  42% with 0 failures

 Completed [==================>-------------------------]  44% with 0 failures

 Completed [===================>------------------------]  46% with 0 failures

 Completed [====================>-----------------------]  47% with 0 failures

 Completed [=====================>----------------------]  49% with 0 failures

 Completed [=====================>----------------------]  51% with 0 failures

 Completed [======================>---------------------]  53% with 0 failures

 Completed [=======================>--------------------]  54% with 0 failures

 Completed [========================>-------------------]  56% with 0 failures

 Completed [========================>-------------------]  58% with 0 failures

 Completed [=========================>------------------]  59% with 0 failures

 Completed [==========================>-----------------]  61% with 0 failures

 Completed [===========================>----------------]  63% with 0 failures

 Completed [===========================>----------------]  64% with 0 failures

 Completed [============================>---------------]  66% with 0 failures

 Completed [=============================>--------------]  68% with 0 failures

 Completed [==============================>-------------]  69% with 0 failures

 Completed [==============================>-------------]  71% with 0 failures

 Completed [===============================>------------]  73% with 0 failures

 Completed [================================>-----------]  75% with 0 failures

 Completed [=================================>----------]  76% with 0 failures

 Completed [=================================>----------]  78% with 0 failures

 Completed [==================================>---------]  80% with 0 failures

 Completed [===================================>--------]  81% with 0 failures

 Completed [====================================>-------]  83% with 0 failures

 Completed [====================================>-------]  85% with 0 failures

 Completed [=====================================>------]  86% with 0 failures

 Completed [======================================>-----]  88% with 0 failures

 Completed [=======================================>----]  90% with 0 failures

 Completed [=======================================>----]  92% with 0 failures

 Completed [========================================>---]  93% with 0 failures

 Completed [=========================================>--]  95% with 0 failures

 Completed [==========================================>-]  97% with 0 failures

 Completed [==========================================>-]  98% with 0 failures

 Completed [============================================] 100% with 0 failures
                                                                              


Done!

Combining coefficients and standard errors

Calculating log-fold changes

Refitting on reduced model...


 Completed [==>-----------------------------------------]   7% with 0 failures

 Completed [===>----------------------------------------]   8% with 0 failures

 Completed [===>----------------------------------------]  10% with 0 failures

 Completed [====>---------------------------------------]  12% with 0 failures

 Completed [=====>--------------------------------------]  14% with 0 failures

 Completed [======>-------------------------------------]  15% with 0 failures

 Completed [======>-------------------------------------]  17% with 0 failures

 Completed [=======>------------------------------------]  19% with 0 failures

 Completed [========>-----------------------------------]  20% with 0 failures

 Completed [=========>----------------------------------]  22% with 0 failures

 Completed [=========>----------------------------------]  24% with 0 failures

 Completed [==========>---------------------------------]  25% with 0 failures

 Completed [===========>--------------------------------]  27% with 0 failures

 Completed [============>-------------------------------]  29% with 0 failures

 Completed [============>-------------------------------]  31% with 0 failures

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TAP_DE <- rbind(TAP_DE, output)

Run Suerat Test (region)

gRNA_scheme <- t(as.matrix(rc.integrated@meta.data[,grep("^Region", colnames(rc.integrated@meta.data))]))

table(gRNA_scheme[1,])

apply(gRNA_scheme,1,table)[,"Region_99"]

output <- lapply(rownames(gRNA_scheme), runSeuratTest, object = rc.integrated, covariate = ngenes)
output <- do.call(rbind, output)

TAP_DE <- rbind(TAP_DE, output)
write.csv(TAP_DE, "./TAP_DE_aaf800_SCT_202212.csv", row.names=F)

Output

TAP_DE <- read.csv("./TAP_DE_aaf800_SCT_202212.csv")
br_anno <- read.table("../../CW_data/Dusa/new_rhapsody_regions_bins_guides_results.txt", sep="\t", header=TRUE)
br_anno <- br_anno[which((br_anno$class != "NEG-CONTROL") & (br_anno$class != "non-targctrl")),]
br_anno <- br_anno[!is.na(match(br_anno$Rhapsody_name, colnames(rc.integrated@meta.data))),]

adj_pval <- as_tibble(TAP_DE) %>% dplyr::select(gene, ident, p_val_adj) %>% pivot_wider(names_from = ident, values_from = p_val_adj, values_fill = 1)

write.table(adj_pval, "adj_pvalue_mtx_aaf800_SCT_202212.txt", quote = FALSE, row.names = FALSE, sep="\t")

TAP_DE$significance <- TAP_DE$p_val_adj
TAP_DE$significance[which(TAP_DE$p_val_adj < 0.05)] = "<0.05" 
TAP_DE$significance[which(TAP_DE$p_val_adj >= 0.05)] = ">=0.05"

Number of gene per cell/ Number of cell per gene

sct <- as.matrix(rc.integrated@assays$SCT@data)

summary(colSums(sct))

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  12.14   29.60   32.75   32.96   36.19   53.66 

boxplot(colSums(sct))

## Captured genes per cell
summary(colSums(sct>0))

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      4      15      17      17      19      29 

boxplot(colSums(sct>0))

## Cells per gene
summary(rowSums(sct>0))

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
    3.0   172.5  1227.0  4765.3  8414.0 16535.0 

nc <- rowSums(sct>0)

names(nc) <- rownames(sct)

## Number of cells per gene
#sort(nc)
summary(nc)

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
    3.0   172.5  1227.0  4765.3  8414.0 16535.0 

## Genes that are expressed in less than 50 cells
sort(nc[which(nc < 50)])

AC111006.1

3

AC108210.1

6

LINC02475

11

TLR10

12

YIPF7

16

AC024022.1

18

RPL12P20

24

UCHL1.AS1

28

AC096734.2

32

AC105389.3

32

UCHL1

33

ZBTB12BP

38

boxplot(nc)

dat <- data.frame(gene=names(nc), number_of_cells=as.numeric(nc))

dat <- dat %>% arrange(desc(number_of_cells))

dat <- within(dat, gene <- factor(gene, levels= names(sort(nc,decreasing = FALSE))))

options(repr.plot.width=8, repr.plot.height=12)
ggplot(dat, aes(x=gene, y=number_of_cells)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=12),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Nr of cells in which expression is detected")+ coord_flip() + scale_y_continuous(labels = comma, breaks=c(0,5000,10000,15000,20000))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

Combinatorial effect

## APBB2 
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="APBB2") %>% filter (significance=="<0.05")

A data.frame: 3 × 10

p_val	avg_logFC	pct.1	pct.2	p_val_adj	gene	ident	method	ncells	significance
<dbl>	<dbl>	<lgl>	<lgl>	<dbl>	<chr>	<chr>	<chr>	<int>	<chr>
4.906618e-04	0.02617787	NA	NA	2.894905e-02	APBB2	Region_174	MAST.cov	18	<0.05
3.544565e-15	0.02304408	NA	NA	2.091293e-13	APBB2	Region_233	MAST.cov	187	<0.05
1.301152e-29	0.04381527	NA	NA	7.676797e-28	APBB2	Region_52	MAST.cov	98	<0.05

## CHRNA9 
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="CHRNA9") %>% filter (significance=="<0.05")

A data.frame: 4 × 10

p_val	avg_logFC	pct.1	pct.2	p_val_adj	gene	ident	method	ncells	significance
<dbl>	<dbl>	<lgl>	<lgl>	<dbl>	<chr>	<chr>	<chr>	<int>	<chr>
3.809137e-06	2.931564e-03	NA	NA	2.247391e-04	CHRNA9	Region_250	MAST.cov	52	<0.05
1.307263e-03	-1.274773e-06	NA	NA	2.570951e-02	CHRNA9	Region_663	MAST.cov	131	<0.05
1.283842e-05	1.182990e-03	NA	NA	7.574667e-04	CHRNA9	Region_668	MAST.cov	50	<0.05
2.797089e-10	1.815131e-03	NA	NA	1.650283e-08	CHRNA9	Region_679	MAST.cov	105	<0.05

## LINC00682 
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="LINC00682") %>% filter (significance=="<0.05")

A data.frame: 5 × 10

p_val	avg_logFC	pct.1	pct.2	p_val_adj	gene	ident	method	ncells	significance
<dbl>	<dbl>	<lgl>	<lgl>	<dbl>	<chr>	<chr>	<chr>	<int>	<chr>
8.232078e-04	0.29052319	NA	NA	4.856926e-02	LINC00682	Region_362	MAST.cov	37	<0.05
2.531771e-07	-0.05617795	NA	NA	7.468725e-06	LINC00682	Region_530	MAST.cov	550	<0.05
1.250357e-04	-0.07342540	NA	NA	3.688555e-03	LINC00682	Region_537	MAST.cov	369	<0.05
3.373659e-04	0.11022913	NA	NA	9.952295e-03	LINC00682	Region_553	MAST.cov	88	<0.05
4.408327e-11	0.13827910	NA	NA	2.600913e-09	LINC00682	Region_564	MAST.cov	181	<0.05

## BEND4 
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="BEND4") %>% filter (significance=="<0.05")

A data.frame: 4 × 10

p_val	avg_logFC	pct.1	pct.2	p_val_adj	gene	ident	method	ncells	significance
<dbl>	<dbl>	<lgl>	<lgl>	<dbl>	<chr>	<chr>	<chr>	<int>	<chr>
1.804165e-16	0.05449940	NA	NA	1.064458e-14	BEND4	Region_669	MAST.cov	67	<0.05
4.539835e-164	0.23330717	NA	NA	2.678503e-162	BEND4	Region_671	MAST.cov	266	<0.05
2.426224e-09	0.03702678	NA	NA	1.431472e-07	BEND4	Region_730	MAST.cov	97	<0.05
1.608772e-03	0.01909721	NA	NA	4.745879e-02	BEND4	Region_740	MAST.cov	144	<0.05

zmtx <- matrix(0, 4, ncol(rc.integrated))
zmtx[1,which((rc.integrated$Region_669=="perturbed"))]=1
zmtx[2,which((rc.integrated$Region_671=="perturbed"))]=1
zmtx[3,which((rc.integrated$Region_730=="perturbed"))]=1
zmtx[4,which((rc.integrated$Region_740=="perturbed"))]=1

idx_1R=which(colSums(zmtx)==1)
idx_XR=which(colSums(zmtx)>1)
## 574 cells have only one region perturbed, 0 cells have more than one regions perturbed
length(idx_1R)
length(idx_XR)

574

0

gene_name <- "BEND4"

#pos_idx <- as.numeric(which(apply(rc.integrated@meta.data[pr_anno$name[which(pr_anno$prom_name==gene_name)]],1, function(x) sum(which(x=="perturbed")))>=1))
pt <- rep("Others", ncol(rc.integrated))
pt[idx_1R] <- "1 region"
pt[idx_XR] <- ">1 region"
dat <- data.frame(expression_level = rc.integrated@assays$SCT@data[gene_name,], region_targeted = pt)
kruskal.test(expression_level~region_targeted, data = dat)
#wilcox.test(dat$expression_level[which(dat$promoter_targeted=="No")], dat$expression_level[which(dat$promoter_targeted=="Yes")])
options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(x=region_targeted, y=expression_level, color=region_targeted)) + 
  geom_boxplot(outlier.shape=NA)+ theme_classic() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

	Kruskal-Wallis rank sum test

data:  expression_level by region_targeted
Kruskal-Wallis chi-squared = 426.33, df = 1, p-value < 2.2e-16

summary(dat$expression_level[which(dat$region_targeted=="Others")])
summary(dat$expression_level[which(dat$region_targeted=="1 region")])
summary(dat$expression_level[which(dat$region_targeted==">1 region")])

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.0000  0.0000  0.0000  0.1649  0.0000  3.1781 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.0000  0.0000  0.0000  0.7891  1.3863  4.2195 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
                                                

wilcox.test(dat$expression_level[which(dat$region_targeted=="1 region")], dat$expression_level[which(dat$region_targeted=="Others")])

	Wilcoxon rank sum test with continuity correction

data:  dat$expression_level[which(dat$region_targeted == "1 region")] and dat$expression_level[which(dat$region_targeted == "Others")]
W = 6061126, p-value < 2.2e-16
alternative hypothesis: true location shift is not equal to 0

## SHISA3 
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="SHISA3") %>% filter (significance=="<0.05")

A data.frame: 15 × 10

p_val	avg_logFC	pct.1	pct.2	p_val_adj	gene	ident	method	ncells	significance
<dbl>	<dbl>	<lgl>	<lgl>	<dbl>	<chr>	<chr>	<chr>	<int>	<chr>
1.706291e-04	0.06587107	NA	NA	1.006712e-02	SHISA3	Region_729	MAST.cov	126	<0.05
4.558646e-04	0.07869602	NA	NA	1.344801e-02	SHISA3	Region_730	MAST.cov	97	<0.05
3.427523e-05	0.08552611	NA	NA	2.022239e-03	SHISA3	Region_738	MAST.cov	119	<0.05
7.184807e-12	0.11627863	NA	NA	4.239036e-10	SHISA3	Region_740	MAST.cov	144	<0.05
1.635408e-08	0.11050001	NA	NA	9.648908e-07	SHISA3	Region_741	MAST.cov	91	<0.05
2.198444e-07	0.15529873	NA	NA	1.297082e-05	SHISA3	Region_780	MAST.cov	12	<0.05
1.630724e-04	0.21047513	NA	NA	9.621269e-03	SHISA3	Region_789	MAST.cov	19	<0.05
8.211968e-86	0.69050674	NA	NA	4.845061e-84	SHISA3	Region_790	MAST.cov	182	<0.05
2.704311e-05	0.07050796	NA	NA	1.595544e-03	SHISA3	Region_803	MAST.cov	138	<0.05
7.693940e-06	0.11021861	NA	NA	4.539425e-04	SHISA3	Region_806	MAST.cov	108	<0.05
1.231370e-04	0.17262495	NA	NA	7.265086e-03	SHISA3	Region_816	MAST.cov	43	<0.05
2.812233e-08	0.10472029	NA	NA	1.659218e-06	SHISA3	Region_828	MAST.cov	79	<0.05
1.644173e-20	0.33153781	NA	NA	9.700622e-19	SHISA3	Region_829	MAST.cov	49	<0.05
9.455928e-12	0.27819800	NA	NA	5.578998e-10	SHISA3	Region_831	MAST.cov	50	<0.05
1.126435e-05	0.10038970	NA	NA	6.645969e-04	SHISA3	Region_840	MAST.cov	106	<0.05

zmtx <- matrix(0, 15, ncol(rc.integrated))
zmtx[1,which((rc.integrated$Region_729=="perturbed"))]=1
zmtx[2,which((rc.integrated$Region_730=="perturbed"))]=1
zmtx[3,which((rc.integrated$Region_738=="perturbed"))]=1
zmtx[4,which((rc.integrated$Region_740=="perturbed"))]=1
zmtx[5,which((rc.integrated$Region_741=="perturbed"))]=1
zmtx[6,which((rc.integrated$Region_780=="perturbed"))]=1
zmtx[7,which((rc.integrated$Region_789=="perturbed"))]=1
zmtx[8,which((rc.integrated$Region_790=="perturbed"))]=1
zmtx[9,which((rc.integrated$Region_803=="perturbed"))]=1
zmtx[10,which((rc.integrated$Region_806=="perturbed"))]=1
zmtx[11,which((rc.integrated$Region_816=="perturbed"))]=1
zmtx[12,which((rc.integrated$Region_828=="perturbed"))]=1
zmtx[13,which((rc.integrated$Region_829=="perturbed"))]=1
zmtx[14,which((rc.integrated$Region_831=="perturbed"))]=1
zmtx[15,which((rc.integrated$Region_840=="perturbed"))]=1

idx_1R=which(colSums(zmtx)==1)
idx_XR=which(colSums(zmtx)>1)
## 1363 cells have only one region perturbed, 0 cells have more than one regions perturbed
length(idx_1R)
length(idx_XR)

1363

0

gene_name <- "SHISA3"

#pos_idx <- as.numeric(which(apply(rc.integrated@meta.data[pr_anno$name[which(pr_anno$prom_name==gene_name)]],1, function(x) sum(which(x=="perturbed")))>=1))
pt <- rep("Others", ncol(rc.integrated))
pt[idx_1R] <- "1 region"
pt[idx_XR] <- ">1 region"
dat <- data.frame(expression_level = rc.integrated@assays$SCT@data[gene_name,], region_targeted = pt)
kruskal.test(expression_level~region_targeted, data = dat)
#wilcox.test(dat$expression_level[which(dat$promoter_targeted=="No")], dat$expression_level[which(dat$promoter_targeted=="Yes")])
ggplot(dat, aes(x=region_targeted, y=expression_level, color=region_targeted)) + 
  geom_boxplot(outlier.shape=NA)+ theme_classic() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

	Kruskal-Wallis rank sum test

data:  expression_level by region_targeted
Kruskal-Wallis chi-squared = 386.73, df = 1, p-value < 2.2e-16

summary(dat$expression_level[which(dat$region_targeted=="Others")])
summary(dat$expression_level[which(dat$region_targeted=="1 region")])
summary(dat$expression_level[which(dat$region_targeted==">1 region")])

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   0.000   0.000   0.332   0.000   4.663 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   0.000   0.000   0.861   1.609   4.812 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
                                                

wilcox.test(dat$expression_level[which(dat$region_targeted=="1 region")], dat$expression_level[which(dat$region_targeted=="Others")])

	Wilcoxon rank sum test with continuity correction

data:  dat$expression_level[which(dat$region_targeted == "1 region")] and dat$expression_level[which(dat$region_targeted == "Others")]
W = 12859113, p-value < 2.2e-16
alternative hypothesis: true location shift is not equal to 0

## PHOX2B expression
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="PHOX2B") %>% filter (significance=="<0.05")

A data.frame: 13 × 10

p_val	avg_logFC	pct.1	pct.2	p_val_adj	gene	ident	method	ncells	significance
<dbl>	<dbl>	<lgl>	<lgl>	<dbl>	<chr>	<chr>	<chr>	<int>	<chr>
5.421915e-06	0.4677258	NA	NA	3.198930e-04	PHOX2B	Region_477	MAST.cov	116	<0.05
5.047705e-25	-0.5493911	NA	NA	2.978146e-23	PHOX2B	Region_494	MAST.cov	559	<0.05
2.347806e-04	0.3603152	NA	NA	1.385206e-02	PHOX2B	Region_504	MAST.cov	140	<0.05
7.485219e-05	-0.3404573	NA	NA	4.416279e-03	PHOX2B	Region_512	MAST.cov	133	<0.05
1.558321e-04	0.4048890	NA	NA	9.194094e-03	PHOX2B	Region_520	MAST.cov	169	<0.05
1.427880e-12	-0.3854239	NA	NA	8.424490e-11	PHOX2B	Region_530	MAST.cov	550	<0.05
7.026451e-16	-0.3656320	NA	NA	4.145606e-14	PHOX2B	Region_537	MAST.cov	369	<0.05
9.920086e-11	0.8111515	NA	NA	5.852851e-09	PHOX2B	Region_553	MAST.cov	88	<0.05
2.434311e-06	0.6284872	NA	NA	1.436244e-04	PHOX2B	Region_557	MAST.cov	130	<0.05
7.928104e-14	0.5063157	NA	NA	4.677581e-12	PHOX2B	Region_561	MAST.cov	285	<0.05
1.676852e-05	-0.2376408	NA	NA	9.893427e-04	PHOX2B	Region_562	MAST.cov	370	<0.05
1.151785e-08	0.4317661	NA	NA	3.397765e-07	PHOX2B	Region_564	MAST.cov	181	<0.05
9.708373e-06	-0.5605712	NA	NA	5.727940e-04	PHOX2B	Region_99	MAST.cov	70	<0.05

zmtx <- matrix(0, 13, ncol(rc.integrated))
zmtx[1,which((rc.integrated$Region_477=="perturbed"))]=1
zmtx[2,which((rc.integrated$Region_494=="perturbed"))]=1
zmtx[3,which((rc.integrated$Region_504=="perturbed"))]=1
zmtx[4,which((rc.integrated$Region_512=="perturbed"))]=1
zmtx[5,which((rc.integrated$Region_520=="perturbed"))]=1
zmtx[6,which((rc.integrated$Region_530=="perturbed"))]=1
zmtx[7,which((rc.integrated$Region_537=="perturbed"))]=1
zmtx[8,which((rc.integrated$Region_553=="perturbed"))]=1
zmtx[9,which((rc.integrated$Region_557=="perturbed"))]=1
zmtx[10,which((rc.integrated$Region_561=="perturbed"))]=1
zmtx[11,which((rc.integrated$Region_562=="perturbed"))]=1
zmtx[12,which((rc.integrated$Region_564=="perturbed"))]=1
zmtx[13,which((rc.integrated$Region_99=="perturbed"))]=1

idx_1R=which(colSums(zmtx)==1)
idx_XR=which(colSums(zmtx)>1)

## 3152 cells have only one region perturbed, 4 cells have more than one regions perturbed
length(idx_1R)
length(idx_XR)

3152

4

gene_name <- "PHOX2B"

#pos_idx <- as.numeric(which(apply(rc.integrated@meta.data[pr_anno$name[which(pr_anno$prom_name==gene_name)]],1, function(x) sum(which(x=="perturbed")))>=1))
pt <- rep("Others", ncol(rc.integrated))
pt[idx_1R] <- "1 region"
pt[idx_XR] <- ">1 region"
dat <- data.frame(expression_level = rc.integrated@assays$SCT@data[gene_name,], region_targeted = pt)
kruskal.test(expression_level~region_targeted, data = dat)
#wilcox.test(dat$expression_level[which(dat$promoter_targeted=="No")], dat$expression_level[which(dat$promoter_targeted=="Yes")])
ggplot(dat, aes(x=region_targeted, y=expression_level, color=region_targeted)) + geom_boxplot(outlier.shape=NA)+ coord_cartesian(ylim=c(-4,9))+theme_classic() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

	Kruskal-Wallis rank sum test

data:  expression_level by region_targeted
Kruskal-Wallis chi-squared = 234.03, df = 2, p-value < 2.2e-16

gene_name <- "PHOX2B"

#pos_idx <- as.numeric(which(apply(rc.integrated@meta.data[pr_anno$name[which(pr_anno$prom_name==gene_name)]],1, function(x) sum(which(x=="perturbed")))>=1))
pt <- rep("Others", ncol(rc.integrated))
pt[idx_1R] <- "1 region"
pt[idx_XR] <- ">1 region"
dat <- data.frame(expression_level = rc.integrated@assays$SCT@data[gene_name,], region_targeted = pt)
kruskal.test(expression_level~region_targeted, data = dat)
#wilcox.test(dat$expression_level[which(dat$promoter_targeted=="No")], dat$expression_level[which(dat$promoter_targeted=="Yes")])
ggplot(dat, aes(x=region_targeted, y=expression_level, color=region_targeted)) + 
  geom_boxplot(outlier.shape=NA)+ theme_classic() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

	Kruskal-Wallis rank sum test

data:  expression_level by region_targeted
Kruskal-Wallis chi-squared = 234.03, df = 2, p-value < 2.2e-16

pdf("PHOX2B_combinatorial_effect_wo_outliers_202212.pdf",width=6,height=6)
ggplot(dat, aes(x=region_targeted, y=expression_level, color=region_targeted)) + 
  geom_boxplot(outlier.shape=NA)+ theme_classic() + ggtitle(gene_name)+ NoLegend()+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()

png: 2

summary(dat$expression_level[which(dat$region_targeted=="Others")])
summary(dat$expression_level[which(dat$region_targeted=="1 region")])
summary(dat$expression_level[which(dat$region_targeted==">1 region")])

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.0000  0.6931  1.9459  1.7839  2.8332  4.7791 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   1.099   2.485   2.164   3.219   4.868 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   0.000   1.354   1.501   2.855   3.296 

wilcox.test(dat$expression_level[which(dat$region_targeted=="1 region")], dat$expression_level[which(dat$region_targeted=="Others")])

	Wilcoxon rank sum test with continuity correction

data:  dat$expression_level[which(dat$region_targeted == "1 region")] and dat$expression_level[which(dat$region_targeted == "Others")]
W = 24749532, p-value < 2.2e-16
alternative hypothesis: true location shift is not equal to 0

wilcox.test(dat$expression_level[which(dat$region_targeted==">1 region")], dat$expression_level[which(dat$region_targeted=="Others")])

	Wilcoxon rank sum test with continuity correction

data:  dat$expression_level[which(dat$region_targeted == ">1 region")] and dat$expression_level[which(dat$region_targeted == "Others")]
W = 24284, p-value = 0.7473
alternative hypothesis: true location shift is not equal to 0

wilcox.test(dat$expression_level[which(dat$region_targeted==">1 region")], dat$expression_level[which(dat$region_targeted=="1 region")])

	Wilcoxon rank sum test with continuity correction

data:  dat$expression_level[which(dat$region_targeted == ">1 region")] and dat$expression_level[which(dat$region_targeted == "1 region")]
W = 4811.5, p-value = 0.4111
alternative hypothesis: true location shift is not equal to 0

ggplot(TAP_DE[grep("^Region", TAP_DE$ident),], aes(x=avg_logFC, y=-log(p_val_adj,10))) + geom_point(aes(colour = significance),size=3)+theme_classic()+xlab("Fold Change (log)")+ylab("Adj-p-value (-log10)")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )

Warning message:
“Removed 3703 rows containing missing values (`geom_point()`).”

pdf("Rhapsody_region_summary_202212.pdf",width=6,height=6)
ggplot(TAP_DE[grep("^Region", TAP_DE$ident),], aes(x=avg_logFC, y=-log(p_val_adj,10))) + geom_point(aes(colour = significance),size=3)+theme_classic()+xlab("Fold Change (log)")+ylab("Adj-p-value (-log10)")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()

Warning message:
“Removed 3703 rows containing missing values (`geom_point()`).”

png: 2

## 1034/1046 gRNA, 222 Region
length(table(TAP_DE[grep("^X",TAP_DE$ident),]$ident))
length(table(TAP_DE[grep("^Region",TAP_DE$ident),]$ident))

1034

222

# Missing gRNA
1046-length(table(TAP_DE$ident[grep("^X",TAP_DE$ident)]))

12

# ncells per gRNA/bin/region (control gRNAs excluded)
summary(TAP_DE$ncells[grep("^X",TAP_DE$ident)], breaks = 100)
#summary(TAP_DE$ncells[grep("^PHOX",TAP_DE$ident)], breaks = 100)
summary(TAP_DE$ncells[grep("^Region",TAP_DE$ident)], breaks = 100)

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   4.00   13.00   16.00   16.99   21.00   50.00 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   7.00   39.00   61.00   76.37   90.00  559.00 

# Significance level 0.05
hits <- TAP_DE %>% filter(method=="MAST.cov") %>% filter(p_val_adj < 0.05)
ghits <- hits[grep("^X",hits$ident),]
#bhits <- hits[grep("^PHOX", hits$ident),]
rhits <- hits[grep("^Region", hits$ident),]

# number of DE genes
length(table(ghits$gene))
#length(table(bhits$gene))
length(table(rhits$gene))

44

33

length(unique(rhits$ident))

60

sum(table(rhits$ident)>1)

22

table(ghits$gene)

AC095057.3 AC096586.1 AC098590.1 AC098591.1 AC098591.2 AC105389.1 AC105389.3 
         3          5          3          4          3          6          1 
AC108471.2      APBB2    ARL4AP2   ATP1B1P1     ATP8A1      BEND4     CHRNA9 
         2          9          3          3          6         20          9 
   DCAF4L1   FAM114A1     GNPDA2       GUF1      KLHL5   KRT18P25       LIAS 
         1          1          4          2          1          8          5 
    LIMCH1  LINC00682  LINC02265      N4BP2  NDUFB4P12      NSUN7   PABPC1P1 
         2          8          3          3          6          4          6 
     PDS5A     PHOX2B      RBM47       RFC1     RPS7P7     SHISA3    SLC30A9 
         2         20          4          2          3         30          2 
    SMIM14       TLR1       TLR6    TMEM156     TMEM33  UCHL1.AS1       UGDH 
         2          6          2          4          1          1          3 
     WDR19   ZBTB12BP 
         4          1 

# sig pairs
nrow(ghits)
#nrow(bhits)
nrow(rhits)

218

92

PHOX2B_ghits <- ghits %>% filter(gene=="PHOX2B")
#PHOX2B_bhits <- bhits %>% filter(gene=="PHOX2B")
PHOX2B_rhits <- rhits %>% filter(gene=="PHOX2B")

PHOX2B_rhits

A data.frame: 13 × 10

p_val	avg_logFC	pct.1	pct.2	p_val_adj	gene	ident	method	ncells	significance
<dbl>	<dbl>	<lgl>	<lgl>	<dbl>	<chr>	<chr>	<chr>	<int>	<chr>
5.421915e-06	0.4677258	NA	NA	3.198930e-04	PHOX2B	Region_477	MAST.cov	116	<0.05
5.047705e-25	-0.5493911	NA	NA	2.978146e-23	PHOX2B	Region_494	MAST.cov	559	<0.05
2.347806e-04	0.3603152	NA	NA	1.385206e-02	PHOX2B	Region_504	MAST.cov	140	<0.05
7.485219e-05	-0.3404573	NA	NA	4.416279e-03	PHOX2B	Region_512	MAST.cov	133	<0.05
1.558321e-04	0.4048890	NA	NA	9.194094e-03	PHOX2B	Region_520	MAST.cov	169	<0.05
1.427880e-12	-0.3854239	NA	NA	8.424490e-11	PHOX2B	Region_530	MAST.cov	550	<0.05
7.026451e-16	-0.3656320	NA	NA	4.145606e-14	PHOX2B	Region_537	MAST.cov	369	<0.05
9.920086e-11	0.8111515	NA	NA	5.852851e-09	PHOX2B	Region_553	MAST.cov	88	<0.05
2.434311e-06	0.6284872	NA	NA	1.436244e-04	PHOX2B	Region_557	MAST.cov	130	<0.05
7.928104e-14	0.5063157	NA	NA	4.677581e-12	PHOX2B	Region_561	MAST.cov	285	<0.05
1.676852e-05	-0.2376408	NA	NA	9.893427e-04	PHOX2B	Region_562	MAST.cov	370	<0.05
1.151785e-08	0.4317661	NA	NA	3.397765e-07	PHOX2B	Region_564	MAST.cov	181	<0.05
9.708373e-06	-0.5605712	NA	NA	5.727940e-04	PHOX2B	Region_99	MAST.cov	70	<0.05

#CaRE vs #gene

table(table(ghits$ident))

  1   2   3   5 
147  23   5   2 

par(mar = c(5, 5, 2, 2))
barplot(table(table(ghits$ident)), xlab="number of differentially expressed gene", ylab="number of gRNA", cex.lab=1.5)
cat("gRNA that regulates 2 genes")
names(which(table(ghits$ident)==2))
cat("gRNA that regulates 3 genes")
names(which(table(ghits$ident)==3))

gRNA that regulates 2 genes

1. 'X124'
2. 'X173'
3. 'X214'
4. 'X283'
5. 'X341'
6. 'X350'
7. 'X356'
8. 'X380'
9. 'X404'
10. 'X572'
11. 'X624'
12. 'X634'
13. 'X651'
14. 'X698'
15. 'X717'
16. 'X74'
17. 'X780'
18. 'X854'
19. 'X882'
20. 'X893'
21. 'X936'
22. 'X942'
23. 'X977'

gRNA that regulates 3 genes

1. 'X185'
2. 'X512'
3. 'X58'
4. 'X829'
5. 'X886'

ggplot(data.frame(table(table(ghits$ident))), aes(x=Var1, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("number of differentially expressed gene")+ylab("number of gRNA")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )

pdf("number_of_DE_per_gRNA_202212.pdf",width=6,height=6)
ggplot(data.frame(table(table(ghits$ident))), aes(x=Var1, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("number of differentially expressed gene")+ylab("number of gRNA")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()

png: 2

data.frame(table(table(rhits$gene)))

A data.frame: 7 × 2

Var1	Freq
<fct>	<int>
1	14
2	8
3	4
4	3
5	2
13	1
15	1

table(rhits$gene)

AC095057.3 AC096586.1 AC096586.2 AC096734.2 AC098590.1 AC098591.1 AC105389.1 
         1          1          1          1          1          1          1 
     APBB2    ARL4AP2     ATP8A1      BEND4     CHRNA9     GNPDA2   KRT18P25 
         3          2          3          4          4          2          3 
 LINC00682  LINC02265      N4BP2  NDUFB4P12      NSUN7   PABPC1P1      PDS5A 
         5          4          1          2          2          2          1 
    PHOX2B      RBM47     RPS7P7     SHISA3    SLC30A9       TLR1       TLR6 
        13          1          5         15          2          3          2 
   TMEM156     TMEM33       UGDH      WDR19   ZBTB12BP 
         2          1          1          1          1 

data.frame(table(table(rhits$ident)))

A data.frame: 5 × 2

Var1	Freq
<fct>	<int>
1	38
2	15
3	5
4	1
5	1

options(repr.plot.width=8, repr.plot.height=8)
ggplot(data.frame(table(table(rhits$gene))), aes(x=Var1, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("Number of CaREs")+ylab("Number of differentially expressed gene")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )

pdf("number_of_region_per_DE_202212.pdf",width=6,height=6)
ggplot(data.frame(table(table(rhits$gene))), aes(x=Var1, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("Number of CaREs")+ylab("Number of differentially expressed gene")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()

png: 2

ggplot(data.frame(table(table(rhits$ident))), aes(x=Var1, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("number of differentially expressed gene")+ylab("number of CaREs")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )

pdf("number_of_DE_per_region_202212.pdf",width=6,height=6)
ggplot(data.frame(table(table(rhits$ident))), aes(x=Var1, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("number of differentially expressed gene")+ylab("number of CaREs")+
  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()

png: 2

# New
barplot(table(table(rhits$ident)), xlab="number of differentially expressed gene", ylab="numer of regions", cex.lab=1.5)
cat("region that regulates 2 genes")
names(which(table(rhits$ident)==2))

region that regulates 2 genes

1. 'Region_132'
2. 'Region_3'
3. 'Region_33'
4. 'Region_494'
5. 'Region_530'
6. 'Region_537'
7. 'Region_553'
8. 'Region_65'
9. 'Region_671'
10. 'Region_679'
11. 'Region_729'
12. 'Region_730'
13. 'Region_740'
14. 'Region_935'
15. 'Region_99'

nr genes/CaRE & nr CaRE/genes (On average, one gene/CaRE regulates one gene's exp)

dat <- data.frame(treatment=rep("gRNA", length(as.numeric(table(ghits$ident)))), nr_gene_per_CaRE=as.numeric(table(ghits$ident)))
#dat <- rbind(dat, data.frame(treatment=rep("bin", length(as.numeric(table(bhits$ident)))), nr_gene_per_CaRE=as.numeric(table(bhits$ident))))
dat <- rbind(dat, data.frame(treatment=rep("region", length(as.numeric(table(rhits$ident)))), nr_gene_per_CaRE=as.numeric(table(rhits$ident))))
dat <- within(dat, treatment <- factor(treatment, levels= c("gRNA","region")))

options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, nr_gene_per_CaRE)) + geom_boxplot() + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

pdf("nr_gene_per_CaRE_2_counts_202212.pdf",width=6,height=6)
ggplot(dat, aes(treatment, nr_gene_per_CaRE)) + geom_boxplot() + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()

png: 2

##On average, one gene/CaRE regulates one gene's exp
cat("gRNA")
summary(as.numeric(table(ghits$ident)))
#cat("bin")
#summary(as.numeric(table(bhits$ident)))
cat("region")
summary(as.numeric(table(rhits$ident)))

gRNA

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  1.000   1.000   1.000   1.232   1.000   5.000 

region

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  1.000   1.000   1.000   1.533   2.000   5.000 

## 22 CaRE regulates more than 1 gene's exp
length(which(as.numeric(table(rhits$ident))>1))

22

dat <- data.frame(treatment=rep("gRNA", length(as.numeric(table(ghits$gene)))), nr_CaRE_per_gene=as.numeric(table(ghits$gene)))
#dat <- rbind(dat, data.frame(treatment=rep("bin", length(as.numeric(table(bhits$gene)))), nr_CaRE_per_gene=as.numeric(table(bhits$gene))))
dat <- rbind(dat, data.frame(treatment=rep("region", length(as.numeric(table(rhits$gene)))), nr_CaRE_per_gene=as.numeric(table(rhits$gene))))
dat <- within(dat, treatment <- factor(treatment, levels= c("gRNA","region")))

options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat, aes(treatment, nr_CaRE_per_gene)) + geom_boxplot() + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

pdf("nr_CaRE_per_gene_2counts_202212.pdf",width=6,height=6)
ggplot(dat, aes(treatment, nr_CaRE_per_gene)) + geom_boxplot() + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()

png: 2

dat_g <- dat %>% filter(treatment=="gRNA")
dat_r <- dat %>% filter(treatment=="region")

options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat_g, aes(treatment, nr_CaRE_per_gene)) + geom_boxplot() + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

pdf("nr_CaRE_per_gene_2counts_gRNA_202212.pdf",width=6,height=6)
ggplot(dat_g, aes(treatment, nr_CaRE_per_gene)) + geom_boxplot() + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()

png: 2

options(repr.plot.width=8, repr.plot.height=8)
ggplot(dat_r, aes(treatment, nr_CaRE_per_gene)) + geom_boxplot() + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

pdf("nr_CaRE_per_gene_2counts_region_202212.pdf",width=6,height=6)
ggplot(dat_r, aes(treatment, nr_CaRE_per_gene)) + geom_boxplot() + theme_minimal() +
  theme(axis.title.x=element_blank(),axis.text.x = element_text(size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()

png: 2

## On average, a gene is regulated by 2-3 CaREs
cat("gRNA")
summary(as.numeric(table(ghits$gene)))
#cat("bin")
#summary(as.numeric(table(bhits$gene)))
cat("region")
summary(as.numeric(table(rhits$gene)))

gRNA

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  1.000   2.000   3.000   4.955   6.000  30.000 

region

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  1.000   1.000   2.000   2.788   3.000  15.000 

dat <- data.frame(care = names(sort(table(ghits$ident),decreasing = FALSE)), nr_gene = as.numeric(sort(table(ghits$ident),decreasing = FALSE)))
dat <- within(dat, care <- factor(care, levels= names(sort(table(ghits$ident),decreasing = FALSE))))

nrow(dat)

177

dat <- dat[162:177,]

options(repr.plot.width=8, repr.plot.height=12)
ggplot(dat, aes(x=care, y=nr_gene)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant DE genes")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

pdf("DE_gRNA_2counts_202212.pdf",width=6,height=9)
ggplot(dat, aes(x=care, y=nr_gene)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant DE genes")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()

png: 2

dat <- data.frame(care = names(sort(table(rhits$ident),decreasing = FALSE)), nr_gene = as.numeric(sort(table(rhits$ident),decreasing = FALSE)))
dat <- within(dat, care <- factor(care, levels= names(sort(table(rhits$ident),decreasing = FALSE))))

nrow(dat)

60

options(repr.plot.width=8, repr.plot.height=12)
ggplot(dat, aes(x=care, y=nr_gene)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=12),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant DE genes")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

pdf("DE_region_2counts_202212.pdf",width=6,height=9)
ggplot(dat, aes(x=care, y=nr_gene)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=12),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant DE genes")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()

png: 2

dat <- data.frame(gene = names(sort(table(ghits$gene),decreasing = FALSE)), nr_care = as.numeric(sort(table(ghits$gene),decreasing = FALSE)))
dat <- within(dat, gene <- factor(gene, levels= names(sort(table(ghits$gene),decreasing = FALSE))))

options(repr.plot.width=8, repr.plot.height=12)
ggplot(dat, aes(x=gene, y=nr_care)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant gRNAs")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

pdf("DE_gRNA_gene_2counts_202212.pdf",width=6,height=9)
ggplot(dat, aes(x=gene, y=nr_care)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant gRNAs")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()

png: 2

dat <- data.frame(gene = names(sort(table(rhits$gene),decreasing = FALSE)), nr_care = as.numeric(sort(table(rhits$gene),decreasing = FALSE)))
dat <- within(dat, gene <- factor(gene, levels= names(sort(table(rhits$gene),decreasing = FALSE))))

options(repr.plot.width=8, repr.plot.height=12)
ggplot(dat, aes(x=gene, y=nr_care)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant CaREs")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

pdf("DE_region_gene_2counts_202212.pdf",width=6,height=9)
ggplot(dat, aes(x=gene, y=nr_care)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant CaREs")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()

png: 2

## Genes having less than 50 genes expressed
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="AC108210.1") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="Y1PF7") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="RPL12P20") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="UCHL1.AS1") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="UCHL1") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="LINC02475") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="TLR10") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="AC024022.1") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="AC105389.3") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="AC111006.1") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="AC096734.2") %>% filter (significance=="<0.05")
TAP_DE[grep("^Region",TAP_DE$ident),] %>% filter(gene=="ZBTB12BP") %>% filter (significance=="<0.05")

A data.frame: 0 × 10

p_val	avg_logFC	pct.1	pct.2	p_val_adj	gene	ident	method	ncells	significance
<dbl>	<dbl>	<lgl>	<lgl>	<dbl>	<chr>	<chr>	<chr>	<int>	<chr>

A data.frame: 0 × 10

p_val	avg_logFC	pct.1	pct.2	p_val_adj	gene	ident	method	ncells	significance
<dbl>	<dbl>	<lgl>	<lgl>	<dbl>	<chr>	<chr>	<chr>	<int>	<chr>

A data.frame: 0 × 10

p_val	avg_logFC	pct.1	pct.2	p_val_adj	gene	ident	method	ncells	significance
<dbl>	<dbl>	<lgl>	<lgl>	<dbl>	<chr>	<chr>	<chr>	<int>	<chr>

A data.frame: 0 × 10

p_val	avg_logFC	pct.1	pct.2	p_val_adj	gene	ident	method	ncells	significance
<dbl>	<dbl>	<lgl>	<lgl>	<dbl>	<chr>	<chr>	<chr>	<int>	<chr>

A data.frame: 0 × 10

p_val	avg_logFC	pct.1	pct.2	p_val_adj	gene	ident	method	ncells	significance
<dbl>	<dbl>	<lgl>	<lgl>	<dbl>	<chr>	<chr>	<chr>	<int>	<chr>

A data.frame: 0 × 10

p_val	avg_logFC	pct.1	pct.2	p_val_adj	gene	ident	method	ncells	significance
<dbl>	<dbl>	<lgl>	<lgl>	<dbl>	<chr>	<chr>	<chr>	<int>	<chr>

A data.frame: 0 × 10

p_val	avg_logFC	pct.1	pct.2	p_val_adj	gene	ident	method	ncells	significance
<dbl>	<dbl>	<lgl>	<lgl>	<dbl>	<chr>	<chr>	<chr>	<int>	<chr>

A data.frame: 0 × 10

p_val	avg_logFC	pct.1	pct.2	p_val_adj	gene	ident	method	ncells	significance
<dbl>	<dbl>	<lgl>	<lgl>	<dbl>	<chr>	<chr>	<chr>	<int>	<chr>

A data.frame: 0 × 10

p_val	avg_logFC	pct.1	pct.2	p_val_adj	gene	ident	method	ncells	significance
<dbl>	<dbl>	<lgl>	<lgl>	<dbl>	<chr>	<chr>	<chr>	<int>	<chr>

A data.frame: 0 × 10

p_val	avg_logFC	pct.1	pct.2	p_val_adj	gene	ident	method	ncells	significance
<dbl>	<dbl>	<lgl>	<lgl>	<dbl>	<chr>	<chr>	<chr>	<int>	<chr>

A data.frame: 1 × 10

p_val	avg_logFC	pct.1	pct.2	p_val_adj	gene	ident	method	ncells	significance
<dbl>	<dbl>	<lgl>	<lgl>	<dbl>	<chr>	<chr>	<chr>	<int>	<chr>
0.0002973645	0.0001065904	NA	NA	0.01754451	AC096734.2	Region_847	MAST.cov	76	<0.05

A data.frame: 1 × 10

p_val	avg_logFC	pct.1	pct.2	p_val_adj	gene	ident	method	ncells	significance
<dbl>	<dbl>	<lgl>	<lgl>	<dbl>	<chr>	<chr>	<chr>	<int>	<chr>
0.0004537973	0.0006368986	NA	NA	0.01338702	ZBTB12BP	Region_729	MAST.cov	126	<0.05

dat <- data.frame(gene = names(sort(table(rhits$gene),decreasing = FALSE)), nr_care = as.numeric(sort(table(rhits$gene),decreasing = FALSE)))
dat <- within(dat, gene <- factor(gene, levels= names(sort(table(rhits$gene),decreasing = FALSE))))

options(repr.plot.width=8, repr.plot.height=12)
ggplot(dat, aes(x=gene, y=nr_care)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant CaREs")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

genes.bed$order <- seq(1,129)

sg <- genes.bed[match(c("TLR10","TLR1","TLR6","FAM114A1","TMEM156","KLHL5","AC079921.2","WDR19","RFC1","LIAS","AC021148.1","UGDH","SMIM14","AC108471.2","UBE2K",
                 "ZBTB12BP","AC098591.1","AC098591.2","PABPC1P1","PDS5A","KRT18P25","N4BP2","AC095057.3","LINC02265","CHRNA9","RBM47","NSUN7","ARL4AP2","APBB2",
                 "UCHL1","UCHL1.AS1","LIMCH1","RPL12P20","AC105389.3","PHOX2B","AC105389.1","LINC00682","AC108210.1","TMEM33","DCAF4L1","AC106052.1","SLC30A9",
                 "ATP1B1P1","AC111006.1","BEND4","AC024022.1","SHISA3","RPS7P7","ATP8A1","AC096734.2","AC096734.1","AC098590.1","NDUFB4P12","LINC02475","GUF1",
                 "YIPF7","AC096586.2","AC096586.1","GNPDA2"),genes.bed$gene),]

sg$order <- seq(1,59)

dat <- left_join(sg, dat, by="gene") %>% arrange(order)

dat$gene <- factor(dat$gene, levels = dat$gene)

options(repr.plot.width=8, repr.plot.height=12)
ggplot(dat, aes(x=gene, y=nr_care)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant CaREs")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

Warning message:
“Removed 26 rows containing missing values (`position_stack()`).”

## Box plot ignoring outliers colored by different categories
plot_box <- function(annotation, value, group, title){
    # Prepare data
    data <- data.frame(
      annotation = annotation,
      value = value,
      group = group
    )
    
  options(repr.plot.width=8, repr.plot.height=12)
  # Create the boxplot
  print(ggplot(data, aes(x = annotation, y = value, fill = group)) +
  #geom_boxplot() +
  coord_flip()+
  geom_boxplot(outlier.shape = NA) +
  #coord_cartesian(ylim = c(0, 9000)) +
  labs(x = "", y = "", title = title, fill = NULL) +
  theme_minimal(base_size=18) +
  theme(axis.text.x = element_text(angle = 0, hjust = 1)) )
    
}

annotation <- c()
value <- c()
group <- c()
for (i in dat$gene){
    annotation <- c(annotation, rep(i,ncol(rc.integrated)))
    value <- c(value,rc.integrated@assays$SCT@data[i,which(rc.integrated$X1=="control")],rc.integrated@assays$SCT@data[i,which(rc.integrated$X1!="control")])
    group <- c(group, rep("Control",length(which(rc.integrated$X1=="control"))), rep("Perturbed",length(which(rc.integrated$X1!="control"))))                                               
}


annotation <- factor(annotation, levels= dat$gene)
group <- factor(group, levels= c("Perturbed", "Control"))

plot_box(annotation, value, group, "Normalized Gene Expression Level")

summary(rowSums(rc.integrated@assays$SCT@data))

    Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
    2.08   146.73  1112.80  9238.29  9419.16 78267.55 

## Define high and low expressed genes, coding and non-coding genes
high_exp_genes <- c("FAM114A1","KLHL5","WDR19","RFC1","LIAS","UGDH","SMIM14","UBE2K","AC098591.1","PDS5A","KRT18P25","N4BP2",
                    "ARL4AP2","APBB2","LIMCH1","PHOX2B","LINC00682","TMEM33","SLC30A9","SHISA3","RPS7P7","ATP8A1","AC098590.1",
                    "NDUFB4P12","GUF1","AC096586.1","GNPDA2")
low_exp_genes <- c("TLR10","TLR1","TLR6","TMEM156","AC079921.2","AC021148.1","AC108471.2","ZBTB12BP","AC098591.2","PABPC1P1",
                  "AC095057.3","LINC02265","CHRNA9","RBM47","NSUN7","UCHL1","UCHL1.AS1","RPL12P20","AC105389.3","AC105389.1",
                  "AC108210.1","DCAF4L1","AC106052.1","ATP1B1P1","AC111006.1","BEND4","AC024022.1","AC096734.2","AC096734.1",
                   "LINC02475","YIPF7","AC096586.2")
coding_genes <- c("TLR10","TLR1","TLR6","FAM114A1","TMEM156","KLHL5","WDR19","RFC1","LIAS","UGDH","SMIM14","UBE2K",
                 "PDS5A","N4BP2","CHRNA9","RBM47","NSUN7","APBB2","UCHL1","LIMCH1","PHOX2B","TMEM33","DCAF4L1","SLC30A9",
                 "BEND4","SHISA3","ATP8A1","GUF1","YIPF7","GNPDA2")
## Including pseudogenes
non_coding_genes <- c("AC098591.1", "AC098590.1", "AC096586.1", "AC079921.2", "AC021148.1", "AC108471.2", "AC098591.2", "AC095057.3",
                      "AC105389.3", "AC105389.1", "AC108210.1", "AC106052.1", "AC111006.1", "AC024022.1", "AC096734.2", "AC096734.1",
                      "AC096586.2", "LINC02475", "LINC00682", "LINC02265", "ATP1B1P1", "PABPC1P1", "NDUFB4P12", "ARL4AP2", "UCHL1.AS1",
                      "RPL12P20", "RPS7P7", "ZBTB12BP", "KRT18P25")

length(low_exp_genes)

32

length(high_exp_genes)

27

length(coding_genes)

30

length(non_coding_genes)

29

dat <- dat %>% filter(nr_care != "NA")

options(repr.plot.width=8, repr.plot.height=12)
ggplot(dat, aes(x=gene, y=nr_care)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant CaREs")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

pdf("DE_region_gene_2counts_20240528.pdf",width=6,height=9)
ggplot(dat, aes(x=gene, y=nr_care)) + geom_bar(stat="identity") + theme_minimal() +
  theme(axis.title.y=element_blank(),axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20)) + 
ylab("Number of significant CaREs")+ coord_flip()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()

png: 2

dat

A data.frame: 33 x 9

chrom	start	stop	gene	score	strand	type	order	nr_care
<chr>	<dbl>	<dbl>	<fct>	<chr>	<chr>	<chr>	<int>	<dbl>
chr4	38790676	38856817	TLR1	.	-	gene	2	3
chr4	38823714	38856817	TLR6	.	-	gene	3	2
chr4	38966743	39032922	TMEM156	.	-	gene	5	2
chr4	39182503	39285810	WDR19	.	+	gene	8	1
chr4	39498754	39528311	UGDH	.	-	gene	12	1
chr4	39770080	39771371	ZBTB12BP	.	-	gene	16	1
chr4	40082982	40083106	AC098591.1	.	+	gene	17	1
chr4	39973443	39974338	PABPC1P1	.	+	gene	19	2
chr4	39822862	39977956	PDS5A	.	-	gene	20	1
chr4	40020239	40021517	KRT18P25	.	+	gene	21	3
chr4	40056849	40158252	N4BP2	.	+	gene	22	1
chr4	40166674	40167831	AC095057.3	.	+	gene	23	1
chr4	40316484	40330419	LINC02265	.	+	gene	24	4
chr4	40335332	40355217	CHRNA9	.	+	gene	25	4
chr4	40423266	40630875	RBM47	.	-	gene	26	1
chr4	40749924	40811184	NSUN7	.	+	gene	27	2
chr4	40786109	40786710	ARL4AP2	.	+	gene	28	2
chr4	40810026	41216714	APBB2	.	-	gene	29	3
chr4	41744081	41748725	PHOX2B	.	-	gene	35	13
chr4	41750344	41757341	AC105389.1	.	+	gene	36	1
chr4	41872746	41882955	LINC00682	.	-	gene	37	5
chr4	41935128	41960803	TMEM33	.	+	gene	39	1
chr4	41990501	42090461	SLC30A9	.	+	gene	42	2
chr4	42110852	42152878	BEND4	.	-	gene	45	4
chr4	42397487	42402487	SHISA3	.	+	gene	47	15
chr4	42471809	42472380	RPS7P7	.	+	gene	48	5
chr4	42408372	42657105	ATP8A1	.	-	gene	49	3
chr4	42657495	42657928	AC096734.2	.	+	gene	50	1
chr4	43410040	43410937	AC098590.1	.	-	gene	52	1
chr4	43898961	43899351	NDUFB4P12	.	+	gene	53	2
chr4	44693945	44694386	AC096586.2	.	-	gene	57	1
chr4	44704404	44704965	AC096586.1	.	+	gene	58	1
chr4	44682199	44726588	GNPDA2	.	-	gene	59	2

rc.integrated

An object of class Seurat 
125 features across 16535 samples within 2 assays 
Active assay: SCT (59 features, 59 variable features)
 1 other assay present: RNA

annotation <- c()
value <- c()
for (i in dat$gene){
    annotation <- c(annotation, rep(i,ncol(rc.integrated)))
    value <- c(value,rc.integrated@assays$SCT@data[i,])
}
annotation <- factor(annotation, levels= dat$gene)

names(table(pr_anno$prom_name))

1. 'BEND4'
2. 'DCAF4L1'
3. 'NSUN7'
4. 'PHOX2B'
5. 'RNU1-49P'
6. 'RP11-109E24.1'
7. 'RP11-227F19.1'
8. 'RP11-227F19.2'
9. 'RP11-457P14.5'
10. 'RP11-457P14.6'
11. 'SHISA3'
12. 'SLC30A9'
13. 'TMEM33'
14. 'UCHL1'
15. 'UCHL1.AS1'

## Box plot ignoring outliers colored by different categories
plot_box <- function(annotation, value, group, title){
    # Prepare data
    data <- data.frame(
      annotation = annotation,
      value = value,
      group = group
    )
    
  options(repr.plot.width=12, repr.plot.height=8)
  # Create the boxplot
  print(ggplot(data, aes(x = annotation, y = value, fill = group)) +
  #geom_boxplot() +
  #coord_flip()+
  geom_boxplot(outlier.shape = NA) +
  #coord_cartesian(ylim = c(0, 9000)) +
  labs(x = "", y = "", title = title, fill = NULL) +
  theme_minimal(base_size=18) +
  theme(axis.text.x = element_text(angle = 60, hjust = 1)) )
    
}

intersect(names(table(pr_anno$prom_name)),dat$gene)

1. 'BEND4'
2. 'NSUN7'
3. 'PHOX2B'
4. 'SHISA3'
5. 'SLC30A9'
6. 'TMEM33'

annotation <- c()
value <- c()
group <- c()
for (i in intersect(names(table(pr_anno$prom_name)),dat$gene)){
    pos_idx <- as.numeric(which(apply(rc.integrated@meta.data[pr_anno$name[which(pr_anno$prom_name==i)]],1, function(x) sum(which(x=="perturbed")))>=1))
    pt <- rep("All other", ncol(rc.integrated))
    pt[pos_idx] <- "TSS" 
    annotation <- c(annotation, rep(i,ncol(rc.integrated)))                                  
    group <- c(group, pt)
    value <- c(value, rc.integrated@assays$SCT@data[i,])                                  
}
group <- factor(group, levels= c("All other", "TSS"))

plot_box(annotation, value, group, "Normalized Gene Expression Level")

#ggplot(dat, aes(x=promoter_targeted, y=expression_level, color=promoter_targeted)) + geom_boxplot(outlier.shape=NA)+ theme_minimal() + ggtitle(gene_name)+ NoLegend()+
#  theme(axis.text.x = element_text(size=20),axis.text.y=element_text(size=20),plot.title = element_text(size=20),
#        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))
#                                  #+ coord_cartesian(ylim = c(0, 10))

## Box plot ignoring outliers colored by different categories
plot_box <- function(annotation, value, title){
    # Prepare data
    data <- data.frame(
      annotation = annotation,
      value = value
    )
    
  options(repr.plot.width=12, repr.plot.height=8)
  # Create the boxplot
  print(ggplot(data, aes(x = annotation, y = value)) +
  geom_boxplot() +
  #geom_boxplot(outlier.shape = NA) +
  #coord_cartesian(ylim = c(0, 9000)) +
  labs(x = "", y = "", title = title, fill = NULL) +
  theme_minimal(base_size=18) +
  theme(axis.text.x = element_text(angle = 70, hjust = 1)) )
    
}

plot_box(annotation, value, "Gene Expression Level")

annotation <- c()
value <- c()
for (i in dat$gene){
    annotation <- c(annotation, rep(i,length(which(rc.integrated$X1=="control"))))
    value <- c(value,rc.integrated@assays$SCT@data[i,which(rc.integrated$X1=="control")])
}
annotation <- factor(annotation, levels= dat$gene)

plot_box(annotation, value, "Normalized Gene Expression Level")

## Box plot ignoring outliers colored by different categories
plot_box <- function(annotation, value, group, title){
    # Prepare data
    data <- data.frame(
      annotation = annotation,
      value = value,
      group = group
    )
    
  options(repr.plot.width=8, repr.plot.height=12)
  # Create the boxplot
  print(ggplot(data, aes(x = annotation, y = value, fill = group)) +
  #geom_boxplot() +
  coord_flip()+
  geom_boxplot(outlier.shape = NA) +
  #coord_cartesian(ylim = c(0, 9000)) +
  labs(x = "", y = "", title = title, fill = NULL) +
  theme_minimal(base_size=18) +
  theme(axis.text.x = element_text(angle = 0, hjust = 1)) )
    
}

annotation <- c()
value <- c()
group <- c()
for (i in dat$gene){
    annotation <- c(annotation, rep(i,ncol(rc.integrated)))
    value <- c(value,rc.integrated@assays$SCT@data[i,which(rc.integrated$X1=="control")],rc.integrated@assays$SCT@data[i,which(rc.integrated$X1!="control")])
    group <- c(group, rep("Control",length(which(rc.integrated$X1=="control"))), rep("Perturbed",length(which(rc.integrated$X1!="control"))))                                               
}


annotation <- factor(annotation, levels= dat$gene)
group <- factor(group, levels= c("Perturbed", "Control"))

plot_box(annotation, value, group, "Normalized Gene Expression Level")

Plot TSS.distance

head(genes.bed)

A data.frame: 6 × 7

	chrom	start	stop	gene	score	strand	type
	<chr>	<dbl>	<dbl>	<chr>	<chr>	<chr>	<chr>
1	chr4	38006783	38007105	MRPS33P2	.	-	gene
2	chr4	38276177	38279880	AC098680.2	.	-	gene
3	chr4	38286993	38287491	AC098680.1	.	+	gene
4	chr4	38366913	38385759	LINC02513	.	+	gene
5	chr4	38390753	38391675	AC024023.1	.	+	gene
6	chr4	38420661	38523180	LINC01258	.	-	gene

chrom1 <- br_anno$Chr[match(TAP_DE$ident, br_anno$Rhapsody_name)]
start1 <- br_anno$guide_start[match(TAP_DE$ident, br_anno$Rhapsody_name)]
end1 <- br_anno$guide_end[match(TAP_DE$ident, br_anno$Rhapsody_name)]
chrom2 <- genes.bed$chrom[match(TAP_DE$gene, genes.bed$gene)]
start2 <- genes.bed$start[match(TAP_DE$gene, genes.bed$gene)]
end2 <- genes.bed$stop[match(TAP_DE$gene, genes.bed$gene)]
name <- paste0(TAP_DE$ident,"_",TAP_DE$gene)
score <- TAP_DE$avg_logFC
strand1 <- br_anno$strand[match(TAP_DE$ident, br_anno$Rhapsody_name)]
strand2 <- genes.bed$strand[match(TAP_DE$gene, genes.bed$gene)]
samplenumber <- as.numeric(as.factor(TAP_DE$gene))
gene <- TAP_DE$gene
gRNA <- TAP_DE$ident
log_pvaladj <- -log(TAP_DE$p_val_adj)
type <- TAP_DE$avg_logFC
type[which(type > 0)] <- "up_regulated"
type[which(type < 0)] <- "down_regulated"
#ALL
TAP_DE.bedpe <- data.frame(chrom1, start1, end1, chrom2, start2, end2, name, score, strand1, strand2, samplenumber, gene, gRNA, log_pvaladj, type)
#TAP_DE.bedpe <- ghits.bedpe[!is.na(TAP_DE.bedpe$score),]
gRNA.bed <- data.frame(chrom=br_anno$Chr, start=br_anno$guide_start, stop=br_anno$guide_end, gene=br_anno$Rhapsody_name, score=".", strand=br_anno$strand, type="gene")

TAP_DE.bedpe <- TAP_DE.bedpe[!is.na(TAP_DE.bedpe$chrom1),]

TAP_DE.bedpe$distance.TSS <- apply(TAP_DE.bedpe, 1, function(x){if(x[9]=="+"&x[10]=="+"){abs(as.numeric(x[2])-as.numeric(x[5]))}else if(x[9]=="+"&x[10]=="-"){abs(as.numeric(x[2])-as.numeric(x[6]))}else if(x[9]=="-"&x[10]=="+"){abs(as.numeric(x[3])-as.numeric(x[5]))}else{abs(as.numeric(x[3])-as.numeric(x[6]))}})

TAP_DE.bedpe$significance <- rep("adj.pval >= 0.05", nrow(TAP_DE.bedpe))
TAP_DE.bedpe$significance[TAP_DE.bedpe$log_pvaladj>1.3] <- "adj.pval < 0.05"

head(TAP_DE.bedpe)

A data.frame: 6 × 17

	chrom1	start1	end1	chrom2	start2	end2	name	score	strand1	strand2	samplenumber	gene	gRNA	log_pvaladj	type	distance.TSS	significance
	<chr>	<int>	<int>	<chr>	<dbl>	<dbl>	<chr>	<dbl>	<chr>	<chr>	<dbl>	<chr>	<chr>	<dbl>	<chr>	<dbl>	<chr>
1	chr4	40790019	40790039	chr4	44682199	44726588	X1_GNPDA2	-0.015279653	+	-	26	GNPDA2	X1	0.008408941	down_regulated	3936569	adj.pval >= 0.05
2	chr4	40790019	40790039	chr4	42471809	42472380	X1_RPS7P7	0.133542942	+	+	44	RPS7P7	X1	0.008408941	up_regulated	1681790	adj.pval >= 0.05
3	chr4	40790019	40790039	chr4	40335332	40355217	X1_CHRNA9	0.001029732	+	+	23	CHRNA9	X1	0.008408941	up_regulated	454687	adj.pval >= 0.05
4	chr4	40790019	40790039	chr4	39045038	39126857	X1_KLHL5	0.012400904	+	+	28	KLHL5	X1	0.008408941	up_regulated	1744981	adj.pval >= 0.05
5	chr4	40790019	40790039	chr4	40166674	40167831	X1_AC095057.3	NA	+	+	4	AC095057.3	X1	0.008408941	NA	623345	adj.pval >= 0.05
6	chr4	40790019	40790039	chr4	41744081	41748725	X1_PHOX2B	-0.001536993	+	-	40	PHOX2B	X1	0.008408941	down_regulated	958706	adj.pval >= 0.05

head(pr_anno)

A data.frame: 6 × 10

	chr	start	end	strand	name	chr_prom	start_prom	end_prom	prom_name	overlap
	<chr>	<int>	<int>	<chr>	<chr>	<chr>	<int>	<int>	<chr>	<int>
1	chr4	40750204	40750224	+	X396	chr4	40749396	40750396	NSUN7	20
2	chr4	41256120	41256140	+	X486	chr4	41255912	41256912	UCHL1	20
3	chr4	41256133	41256153	+	X487	chr4	41255912	41256912	UCHL1	20
4	chr4	41256599	41256619	+	X488	chr4	41256226	41257226	UCHL1.AS1	20
5	chr4	41256599	41256619	+	X488	chr4	41255912	41256912	UCHL1	20
6	chr4	41256611	41256631	+	X489	chr4	41256226	41257226	UCHL1.AS1	20

TAP_DE.bedpe_pr <- full_join(TAP_DE.bedpe, rename(pr_anno, gRNA = name), by = "gRNA")
TAP_DE.bedpe_pr_en <- TAP_DE.bedpe_pr[!is.na(TAP_DE.bedpe_pr$prom_name),] %>% filter(significance=="adj.pval < 0.05") %>% filter(prom_name!=gene)
## 21 gRNA
table(TAP_DE.bedpe_pr_en$gRNA)

X1019  X237  X486  X490  X624  X631  X634  X635  X636  X672  X823  X826  X849 
    1     1     1     1     1     2     8     1     1     3     4     1     1 
 X850  X912  X913  X914  X915 
    3     1     1     3     3 

## Region
table(br_anno$Region_name[match(TAP_DE.bedpe_pr_en$gRNA, br_anno$Rhapsody_name)])

Region_256 Region_494 Region_504 Region_577 Region_582 Region_603 Region_609 
         2         13          3          4          1          1          1 
Region_671 Region_790 
         4          8 

## Check whether genes fall into the genome range covered by gRNA targeting
gRNA_MIN <- min(TAP_DE.bedpe$start1)
gRNA_MAX <- max(TAP_DE.bedpe$end1)
TAP_DE.bedpe$gRNA_covered <- apply(TAP_DE.bedpe, 1, function(x){if(x[5]<=gRNA_MIN & x[6]<= gRNA_MIN){"Not Covered"}else if(x[5]>=gRNA_MAX & x[6]>=gRNA_MAX){"Not Covered"}else {"Covered"}})

table(TAP_DE.bedpe$gRNA_covered)

    Covered Not Covered 
      25850       35156 

options(repr.plot.width=8, repr.plot.height=8)
ggplot(TAP_DE.bedpe, aes(distance.TSS/1000000, log_pvaladj, shape=significance)) +geom_point(aes(colour = gRNA_covered),size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Distance to TSS (Mb)")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
labs(color="gRNA")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

pdf("Distance_to_TSS_vs_pvalue_gRNA_coverage_202212.pdf",width=8,height=6)
ggplot(TAP_DE.bedpe, aes(distance.TSS/1000000, log_pvaladj, shape=significance)) +geom_point(aes(colour = gRNA_covered),size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Distance to TSS (Mb)")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
labs(color="gRNA")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()

png: 2

Sushi

source('plotBedpe.R')
source('convertstrandinfo.R')
source('SushiColors.R')

ghits <- hits[grep("^X",hits$ident),]

chrom1 <- br_anno$Chr[match(ghits$ident, br_anno$Rhapsody_name)]
start1 <- br_anno$guide_start[match(ghits$ident, br_anno$Rhapsody_name)]
end1 <- br_anno$guide_end[match(ghits$ident, br_anno$Rhapsody_name)]
chrom2 <- genes.bed$chrom[match(ghits$gene, genes.bed$gene)]
start2 <- genes.bed$start[match(ghits$gene, genes.bed$gene)]
end2 <- genes.bed$stop[match(ghits$gene, genes.bed$gene)]
name <- paste0(ghits$ident,"_",ghits$gene)
score <- ghits$avg_logFC
strand1 <- br_anno$strand[match(ghits$ident, br_anno$Rhapsody_name)]
strand2 <- genes.bed$strand[match(ghits$gene, genes.bed$gene)]
samplenumber <- as.numeric(as.factor(ghits$gene))
gene <- ghits$gene
gRNA <- ghits$ident
log_pvaladj <- -log(ghits$p_val_adj)
type <- ghits$avg_logFC
type[which(type > 0)] <- "up_regulated"
type[which(type < 0)] <- "down_regulated"
#ALL
ghits.bedpe <- data.frame(chrom1, start1, end1, chrom2, start2, end2, name, score, strand1, strand2, samplenumber, gene, gRNA, log_pvaladj, type)
ghits.bedpe <- ghits.bedpe[!is.na(ghits.bedpe$score),]
gRNA.bed <- data.frame(chrom=br_anno$Chr, start=br_anno$guide_start, stop=br_anno$guide_end, gene=br_anno$Rhapsody_name, score=".", strand=br_anno$strand, type="gene")

ghits.up.bedpe <- ghits.bedpe[which(ghits.bedpe$score>0),]
ghits.down.bedpe <- ghits.bedpe[which(ghits.bedpe$score<0),] 
ghits.down.bedpe$score <- abs(ghits.down.bedpe$score)
genes.up.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.up.bedpe$name))))), genes.bed$gene),]
genes.down.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.down.bedpe$name))))), genes.bed$gene),]
genes.up.bed <- rbind(genes.up.bed, genes.down.bed)
genes.up.bed <- genes.up.bed %>% distinct() %>% arrange(gene)
gRNA.up.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.up.bedpe$name))))), gRNA.bed$gene),]
gRNA.down.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.down.bedpe$name))))), gRNA.bed$gene),]
gRNA.up.bed <- rbind(gRNA.up.bed, gRNA.down.bed)
gRNA.up.bed <- gRNA.up.bed %>% distinct()%>% arrange(gene)

nb.cols <- length(table(c(ghits.up.bedpe$samplenumber,ghits.down.bedpe$samplenumber)))
chrom = "chr4"
chromstart = 38500000
chromend = 44500000

getwd()

'/fast/AG_Ohler/CheWei/kallisto-bus/Dusa_hg38_p13'

#Type
pdf("track_regulation_grna_202212.pdf",width=16,height=4)
options(repr.plot.width=16, repr.plot.height=4)
par(mar = c(2, 4, 0, 4))
pbpe = plotBedpe(ghits.bedpe,chrom,chromstart,chromend,plottype="lines",
colorby=as.numeric(as.factor(ghits.bedpe$type)),
colorbycol=SushiColors(2),flip=TRUE)
legend("right",inset = 0.1,cex=1,text.width=2,legend=names(table(as.character(as.factor(ghits.bedpe$type)))),
col=SushiColors(2)(2),pch=19,bty='n',text.font=2,y.intersp=2)
axis(side=2,labels = FALSE, tick = FALSE)
mtext("regulation",side=2,line=3,cex=1,font=2)
dev.off()

[1] "yes"
[1] "yes"

png: 2

#Log_FoldChange
pdf("track_avg_logFC_grna_202212.pdf",width=16,height=2)
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
heights = ghits.bedpe$score,plottype="loops",
colorby=ghits.bedpe$samplenumber,
colorbycol=colorRampPalette(rev(brewer.pal(nb.cols,"Paired"))),flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("avg_logFC",side=2,line=3,cex=1,font=2)
dev.off()

[1] "yes"
[1] "yes"

png: 2

#GeneTrack
pdf("track_gene_grna_202212.pdf",width=16,height=2.5)
options(repr.plot.width=16, repr.plot.height=1.5)
par(mar = c(0, 4, 0, 4))
pg = suppressWarnings(plotGenes(genes.up.bed,chrom,chromstart,chromend ,
types=genes.up.bed$type,maxrows=10,bheight=0.1,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.4,fontsize=0.8,arrowlength = 0.025,
labeltext=TRUE, col=colorRampPalette(rev(brewer.pal(nb.cols,"Paired")))(nb.cols)))
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gene",side=2,line=3,cex=1,font=2)
dev.off()

[1] "yes"

png: 2

#gRNATRACK
pdf("track_grna_grna_202212.pdf",width=16,height=8)
options(repr.plot.width=16, repr.plot.height=8)
par(mar = c(0, 4, 0, 4))
pg = plotGenes(gRNA.up.bed,chrom,chromstart,chromend ,
types=gRNA.up.bed$type,maxrows=50,bheight=0,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.2,fontsize=0.8,arrowlength = 0.01,
labeltext=TRUE, col=c())
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gRNA",side=2,line=3,cex=1,font=2)
dev.off()

[1] "yes"

png: 2

#pvalue_adjusted
#options(repr.plot.width=16, repr.plot.height=2)
#par(mar = c(0, 4, 2, 4))
#pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
#heights = ghits.bedpe$log_pvaladj,plottype="loops",
#colorby=ghits.bedpe$samplenumber,
#colorbycol=colorRampPalette(rev(brewer.pal(nb.cols,"Paired"))),flip=TRUE))
#lwdby=ghits.bedpe$score
#axis(side=2,las=2,tcl=.2)
#mtext("log(adj_p_value)",side=2,line=3,cex=1,font=2)
#Type
options(repr.plot.width=16, repr.plot.height=4)
par(mar = c(2, 4, 0, 4))
pbpe = plotBedpe(ghits.bedpe,chrom,chromstart,chromend,plottype="lines",
colorby=as.numeric(as.factor(ghits.bedpe$type)),
colorbycol=SushiColors(2),flip=TRUE)
legend("right",inset = 0.1,cex=1,text.width=2,legend=names(table(as.character(as.factor(ghits.bedpe$type)))),
col=SushiColors(2)(2),pch=19,bty='n',text.font=2,y.intersp=2)
axis(side=2,labels = FALSE, tick = FALSE)
mtext("regulation",side=2,line=3,cex=1,font=2)
#Log_FoldChange
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
heights = ghits.bedpe$score,plottype="loops",
colorby=ghits.bedpe$samplenumber,
colorbycol=colorRampPalette(rev(brewer.pal(nb.cols,"Paired"))),flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("avg_logFC",side=2,line=3,cex=1,font=2)
#GeneTrack
options(repr.plot.width=16, repr.plot.height=2.5)
par(mar = c(0, 4, 0, 4))
pg = suppressWarnings(plotGenes(genes.up.bed,chrom,chromstart,chromend ,
types=genes.up.bed$type,maxrows=10,bheight=0.1,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.4,fontsize=0.8,arrowlength = 0.025,
labeltext=TRUE, col=colorRampPalette(rev(brewer.pal(nb.cols,"Paired")))(nb.cols)))
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gene",side=2,line=3,cex=1,font=2)
#gRNATRACK
options(repr.plot.width=16, repr.plot.height=8)
par(mar = c(0, 4, 0, 4))
pg = plotGenes(gRNA.up.bed,chrom,chromstart,chromend ,
types=gRNA.up.bed$type,maxrows=50,bheight=0,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.2,fontsize=0.8,arrowlength = 0.01,
labeltext=TRUE, col=c())
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gRNA",side=2,line=3,cex=1,font=2)

[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"

[1] "yes"

[1] "yes"

Classify promoters

ghits.bedpe$distance.TSS <- apply(ghits.bedpe, 1, function(x){if(x[9]=="+"&x[10]=="+"){abs(as.numeric(x[2])-as.numeric(x[5]))}else if(x[9]=="+"&x[10]=="-"){abs(as.numeric(x[2])-as.numeric(x[6]))}else if(x[9]=="-"&x[10]=="+"){abs(as.numeric(x[3])-as.numeric(x[5]))}else{abs(as.numeric(x[3])-as.numeric(x[6]))}})

pr_range <- data.frame(gene= genes.bed$gene,start= genes.bed$start-200, end= genes.bed$start+200)
whg <- c()
ispr <- c()
whpr <- c()
for (i in 1:nrow(ghits.bedpe)){
    for (j in 1:nrow(pr_range)){
        if((ghits.bedpe$start1[i]>pr_range$start[j] & ghits.bedpe$start1[i]< pr_range$end[j]) | (ghits.bedpe$end1[i]>pr_range$start[j] & ghits.bedpe$end1[i] < pr_range$end[j])){
            ispr <- c(ispr, "Yes")
            whpr <- c(whpr, pr_range$gene[j])
            whg <- c(whg, ghits.bedpe$gRNA[i])
            break()
        } else {
            if(j == nrow(pr_range)){
            ispr <- c(ispr, "No")
            whpr <- c(whpr, "NA")
            whg <- c(whg, ghits.bedpe$gRNA[i])
            }
        }
    }
}
dat <- data.frame(gRNA = whg, gene = whpr, promoter=ispr)
ghits.bedpe$promoter <- dat$gene

table(dat$gene)

    NA SHISA3 
   206      5 

ghits.bedpe %>% filter(promoter!="NA")

A data.frame: 5 x 17

chrom1	start1	end1	chrom2	start2	end2	name	score	strand1	strand2	samplenumber	gene	gRNA	log_pvaladj	type	distance.TSS	promoter
<chr>	<int>	<int>	<chr>	<dbl>	<dbl>	<chr>	<dbl>	<chr>	<chr>	<dbl>	<chr>	<chr>	<dbl>	<chr>	<dbl>	<chr>
chr4	42397447	42397467	chr4	42397487	42402487	X910_SHISA3	0.4664096	+	+	34	SHISA3	X910	4.527663	up_regulated	40	SHISA3
chr4	42397515	42397535	chr4	42397487	42402487	X912_SHISA3	0.9427664	+	+	34	SHISA3	X912	63.549336	up_regulated	28	SHISA3
chr4	42397611	42397631	chr4	42397487	42402487	X913_SHISA3	0.9012685	+	+	34	SHISA3	X913	16.047242	up_regulated	124	SHISA3
chr4	42397641	42397661	chr4	42397487	42402487	X914_SHISA3	1.3704953	+	+	34	SHISA3	X914	83.873479	up_regulated	154	SHISA3
chr4	42397679	42397699	chr4	42397487	42402487	X915_SHISA3	0.6755128	+	+	34	SHISA3	X915	55.427103	up_regulated	192	SHISA3

Jumped genes

ghits.bedpe

A data.frame: 211 x 17

	chrom1	start1	end1	chrom2	start2	end2	name	score	strand1	strand2	samplenumber	gene	gRNA	log_pvaladj	type	distance.TSS	promoter
	<chr>	<int>	<int>	<chr>	<dbl>	<dbl>	<chr>	<dbl>	<chr>	<chr>	<dbl>	<chr>	<chr>	<dbl>	<chr>	<dbl>	<chr>
1	chr4	41259428	41259448	chr4	44678419	44700928	X1002_GUF1	0.0341733215	+	+	18	GUF1	X1002	4.905729	up_regulated	3418991	NA
2	chr4	42194185	42194205	chr4	43410040	43410937	X1027_AC098590.1	-0.2919132455	+	-	3	AC098590.1	X1027	4.115792	down_regulated	1216752	NA
3	chr4	41367930	41367950	chr4	39045038	39126857	X108_KLHL5	-0.0010774513	+	+	19	KLHL5	X108	2.996921	down_regulated	2322892	NA
4	chr4	41395528	41395548	chr4	40020239	40021517	X117_KRT18P25	0.0354084092	+	+	20	KRT18P25	X117	4.639459	up_regulated	1375289	NA
5	chr4	41405614	41405634	chr4	39459003	39485109	X120_LIAS	0.0044690703	+	+	21	LIAS	X120	3.831877	up_regulated	1946611	NA
6	chr4	41405625	41405645	chr4	41872746	41882955	X121_LINC00682	-0.1359951890	+	-	23	LINC00682	X121	3.043304	down_regulated	477330	NA
7	chr4	41414280	41414300	chr4	41220073	41256727	X124_UCHL1.AS1	0.0100892920	+	-	41	UCHL1.AS1	X124	3.004131	up_regulated	157553	NA
8	chr4	41414280	41414300	chr4	40166674	40167831	X124_AC095057.3	0.0008032585	+	+	1	AC095057.3	X124	3.004131	up_regulated	1247606	NA
9	chr4	41494776	41494796	chr4	38790676	38856817	X131_TLR1	0.0029430826	+	-	37	TLR1	X131	4.639811	up_regulated	2637959	NA
10	chr4	40831316	40831336	chr4	40020239	40021517	X15_KRT18P25	0.0377022971	+	+	20	KRT18P25	X15	10.232980	up_regulated	811077	NA
11	chr4	41634845	41634865	chr4	43898961	43899351	X151_NDUFB4P12	-0.5735367217	+	+	26	NDUFB4P12	X151	9.274555	down_regulated	2264116	NA
12	chr4	41660784	41660804	chr4	40020239	40021517	X155_KRT18P25	0.1515830106	+	+	20	KRT18P25	X155	15.869232	up_regulated	1640545	NA
13	chr4	41700339	41700359	chr4	41744081	41748725	X170_PHOX2B	1.2739117586	+	-	30	PHOX2B	X170	3.012733	up_regulated	48386	NA
15	chr4	41754037	41754057	chr4	41872746	41882955	X173_LINC00682	0.4788132176	+	-	23	LINC00682	X173	3.273311	up_regulated	128918	NA
16	chr4	41782524	41782544	chr4	39182503	39285810	X185_WDR19	-0.0084651451	+	+	43	WDR19	X185	3.361500	down_regulated	2600021	NA
17	chr4	41782524	41782544	chr4	40335332	40355217	X185_CHRNA9	0.0025399652	+	+	14	CHRNA9	X185	3.361500	up_regulated	1447192	NA
18	chr4	41782524	41782544	chr4	38867676	38945739	X185_FAM114A1	0.1176303795	+	+	16	FAM114A1	X185	3.017556	up_regulated	2914848	NA
20	chr4	41807130	41807150	chr4	38790676	38856817	X199_TLR1	0.0021884797	+	-	37	TLR1	X199	6.224071	up_regulated	2950313	NA
21	chr4	41809797	41809817	chr4	39973443	39974338	X200_PABPC1P1	0.0017952477	+	+	28	PABPC1P1	X200	4.095850	up_regulated	1836354	NA
22	chr4	40836015	40836035	chr4	42110852	42152878	X21_BEND4	0.0118460488	+	-	13	BEND4	X21	3.104921	up_regulated	1316863	NA
23	chr4	41838797	41838817	chr4	41872746	41882955	X214_LINC00682	0.4489546782	+	-	23	LINC00682	X214	4.285326	up_regulated	44158	NA
24	chr4	41838797	41838817	chr4	41744081	41748725	X214_PHOX2B	1.1657366751	+	-	30	PHOX2B	X214	3.149307	up_regulated	90072	NA
25	chr4	41887891	41887911	chr4	41744081	41748725	X228_PHOX2B	1.4376525900	+	-	30	PHOX2B	X228	3.610373	up_regulated	139166	NA
26	chr4	42040080	42040100	chr4	38790676	38856817	X244_TLR1	0.0041366603	+	-	37	TLR1	X244	4.365186	up_regulated	3183263	NA
27	chr4	42147822	42147842	chr4	40335332	40355217	X254_CHRNA9	0.0043198282	+	+	14	CHRNA9	X254	12.125825	up_regulated	1812490	NA
28	chr4	42149144	42149164	chr4	42110852	42152878	X257_BEND4	0.2175680256	+	-	13	BEND4	X257	20.797436	up_regulated	3734	NA
29	chr4	42149494	42149514	chr4	42110852	42152878	X260_BEND4	0.1327666209	+	-	13	BEND4	X260	16.773563	up_regulated	3384	NA
30	chr4	42165474	42165494	chr4	42110852	42152878	X264_BEND4	0.0135461527	+	-	13	BEND4	X264	10.742606	up_regulated	12596	NA
31	chr4	42184501	42184521	chr4	40316484	40330419	X265_LINC02265	0.0045985942	+	+	24	LINC02265	X265	5.301508	up_regulated	1868017	NA
32	chr4	42184589	42184609	chr4	42397487	42402487	X266_SHISA3	0.0753909420	+	+	34	SHISA3	X266	3.082512	up_regulated	212898	NA
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
188	chr4	42307003	42307023	chr4	42397487	42402487	X898_SHISA3	-2.881370e-03	+	+	34	SHISA3	X898	3.685833	down_regulated	90484	NA
189	chr4	42307029	42307049	chr4	42397487	42402487	X899_SHISA3	3.661259e-01	+	+	34	SHISA3	X899	26.044537	up_regulated	90458	NA
190	chr4	41144007	41144027	chr4	40316484	40330419	X90_LINC02265	2.961355e-03	+	+	24	LINC02265	X90	4.466547	up_regulated	827523	NA
191	chr4	42397447	42397467	chr4	42397487	42402487	X910_SHISA3	4.664096e-01	+	+	34	SHISA3	X910	4.527663	up_regulated	40	SHISA3
192	chr4	42397515	42397535	chr4	42397487	42402487	X912_SHISA3	9.427664e-01	+	+	34	SHISA3	X912	63.549336	up_regulated	28	SHISA3
193	chr4	42397611	42397631	chr4	42397487	42402487	X913_SHISA3	9.012685e-01	+	+	34	SHISA3	X913	16.047242	up_regulated	124	SHISA3
194	chr4	42397641	42397661	chr4	42397487	42402487	X914_SHISA3	1.370495e+00	+	+	34	SHISA3	X914	83.873479	up_regulated	154	SHISA3
195	chr4	42397679	42397699	chr4	42397487	42402487	X915_SHISA3	6.755128e-01	+	+	34	SHISA3	X915	55.427103	up_regulated	192	SHISA3
196	chr4	42398431	42398451	chr4	42397487	42402487	X916_SHISA3	3.474206e-01	+	+	34	SHISA3	X916	3.537265	up_regulated	944	NA
197	chr4	42398576	42398596	chr4	42397487	42402487	X917_SHISA3	6.508450e-01	+	+	34	SHISA3	X917	20.083096	up_regulated	1089	NA
198	chr4	42481603	42481623	chr4	42397487	42402487	X926_SHISA3	2.747485e-01	+	+	34	SHISA3	X926	5.276413	up_regulated	84116	NA
199	chr4	42481619	42481639	chr4	42397487	42402487	X927_SHISA3	1.860490e-01	+	+	34	SHISA3	X927	6.767309	up_regulated	84132	NA
200	chr4	42481716	42481736	chr4	40316484	40330419	X929_LINC02265	1.504744e-03	+	+	24	LINC02265	X929	3.340200	up_regulated	2165232	NA
201	chr4	42488691	42488711	chr4	43898961	43899351	X931_NDUFB4P12	3.842238e-01	+	+	26	NDUFB4P12	X931	3.483382	up_regulated	1410270	NA
202	chr4	42490039	42490059	chr4	40749924	40811184	X936_NSUN7	7.410074e-04	+	+	27	NSUN7	X936	4.030951	up_regulated	1740115	NA
203	chr4	42490039	42490059	chr4	39639106	39666879	X936_AC108471.2	6.022433e-03	+	+	8	AC108471.2	X936	3.087727	up_regulated	2850933	NA
204	chr4	42513914	42513934	chr4	39973443	39974338	X940_PABPC1P1	1.152369e-03	+	+	28	PABPC1P1	X940	4.883506	up_regulated	2540471	NA
205	chr4	42513973	42513993	chr4	40423266	40630875	X942_RBM47	3.030300e-03	+	-	31	RBM47	X942	10.036695	up_regulated	1883098	NA
206	chr4	42513973	42513993	chr4	42397487	42402487	X942_SHISA3	3.267667e-01	+	+	34	SHISA3	X942	4.352914	up_regulated	116486	NA
207	chr4	42718241	42718261	chr4	41750344	41757341	X947_AC105389.1	7.327823e-04	+	+	6	AC105389.1	X947	4.743006	up_regulated	967897	NA
208	chr4	40755892	40755912	chr4	40749924	40811184	X951_NSUN7	8.591669e-04	+	+	27	NSUN7	X951	4.047217	up_regulated	5968	NA
209	chr4	40755979	40755999	chr4	38790676	38856817	X952_TLR1	4.623949e-03	+	-	37	TLR1	X952	5.924312	up_regulated	1899162	NA
210	chr4	40802524	40802544	chr4	40020239	40021517	X955_KRT18P25	1.048582e-01	+	+	20	KRT18P25	X955	14.645500	up_regulated	782285	NA
211	chr4	42396691	42396711	chr4	42397487	42402487	X971_SHISA3	2.104751e-01	+	+	34	SHISA3	X971	4.643779	up_regulated	796	NA
212	chr4	40823804	40823824	chr4	40056849	40158252	X977_N4BP2	1.813326e-01	+	+	25	N4BP2	X977	3.940885	up_regulated	766955	NA
214	chr4	41110270	41110290	chr4	38790676	38856817	X980_TLR1	-9.388096e-05	+	-	37	TLR1	X980	3.311899	down_regulated	2253453	NA
215	chr4	41322807	41322827	chr4	44682199	44726588	X984_GNPDA2	7.046911e-03	+	-	17	GNPDA2	X984	3.746113	up_regulated	3403781	NA
216	chr4	41246288	41246308	chr4	40335332	40355217	X99_CHRNA9	4.876782e-03	+	+	14	CHRNA9	X99	10.941710	up_regulated	910956	NA
217	chr4	41090016	41090036	chr4	44682199	44726588	X997_GNPDA2	1.096161e-01	+	-	17	GNPDA2	X997	4.416889	up_regulated	3636572	NA
218	chr4	42239671	42239691	chr4	42397487	42402487	X1030_SHISA3	1.093835e-01	+	+	34	SHISA3	X1030	6.074699	up_regulated	157816	NA

genes.bed.detected <- genes.bed[genes.bed$gene %in% unique(TAP_DE$gene),]

jumped_gene_counts <- c()
count <- 0
for (i in 1:nrow(ghits.bedpe)){
    for (j in 1:nrow(genes.bed.detected)){
        if(genes.bed.detected$start[j]>=min(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & genes.bed.detected$stop[j]<=max(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & ghits.bedpe$gene[i]!=genes.bed.detected$gene[j]){
            count <- count + 1
        }
        if(j == nrow(genes.bed.detected)){
                jumped_gene_counts <- c(jumped_gene_counts, count)
            count <- 0
        }
   }
}

table(jumped_gene_counts)

jumped_gene_counts
 0  1  2  3  4  5  6  7  8  9 10 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
58 23 12  7  4  4  2  5  4  8  5  3  4  5  4  3  3  4  6  3  3  2  6  7  4  2 
27 28 29 30 31 32 33 34 36 39 40 42 
 4  3  3  2  1  1  1  1  1  1  1  1 

## Skipped genes
length(jumped_gene_counts)-58

153

options(repr.plot.width=8, repr.plot.height=8)
boxplot(jumped_gene_counts, main="number of jumped genes", cex.lab=1.5)
summary(jumped_gene_counts)

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   0.000   5.000   9.758  18.500  42.000 

ggplot(data.frame(table(jumped_gene_counts)), aes(x=jumped_gene_counts, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("Genes jumped")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )

pdf("Genes_jumped_202212.pdf",width=6,height=6)
ggplot(data.frame(table(jumped_gene_counts)), aes(x=jumped_gene_counts, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("Genes jumped")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()

png: 2

barplot(table(jumped_gene_counts), xlab="Genes jumped", ylab="Counts", cex.lab=1.5, border = NA)

ghits.bedpe$jumped_gene_counts <- jumped_gene_counts

sig <- c()
count <- 0
sig_ratio <- c()
for (i in 1:nrow(ghits.bedpe)){
    for (j in 1:nrow(genes.bed.detected)){
        if(genes.bed.detected$start[j]>=min(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & genes.bed.detected$stop[j]<=max(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & ghits.bedpe$gene[i]!=genes.bed.detected$gene[j]){
            count <- count + 1
            sig <- c(sig, if(as.numeric(TAP_DE$p_val_adj[which(TAP_DE$gene == genes.bed.detected$gene[j] & TAP_DE$ident == ghits.bedpe$gRNA[i])])<0.01){"sig"}else{"non_sig"})
        }
        if(j == nrow(genes.bed.detected)){
            sig_ratio <- c(sig_ratio, if(count==0){1}else{length(which(sig=="sig"))/length(sig)})
            sig <- c()
            count <- 0
        }
   }
}

length(sig_ratio)

211

ghits.bedpe$sig_ratio <- sig_ratio

options(repr.plot.width=9.5, repr.plot.height=8)
ggplot(ghits.bedpe, aes(jumped_gene_counts, log_pvaladj))+ geom_point(aes(colour = sig_ratio),size=4) + theme_minimal() + xlab("Genes jumped") + ylab("-log adjusted p-value") + 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 20))+
labs(color="Fraction\nsignificant\ngRNAs")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

options(repr.plot.width=9.5, repr.plot.height=8)
ggplot(ghits.bedpe, aes(jumped_gene_counts, log_pvaladj))+ geom_point(size=4) + theme_minimal() + xlab("Genes jumped") + ylab("-log adjusted p-value") + 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 20))+
labs(color="Fraction\nsignificant\ngRNAs")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

pdf("Genes_jumped_vs_pvalue_202212.pdf",width=6,height=6)
ggplot(ghits.bedpe, aes(jumped_gene_counts, log_pvaladj))+ geom_point(size=4) + theme_minimal() + xlab("Genes jumped") + ylab("-log adjusted p-value") + 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 20))+
labs(color="Fraction\nsignificant\ngRNAs")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()

png: 2

LFC target vs jumped

head(TAP_DE)

A data.frame: 6 × 10

	p_val	avg_logFC	pct.1	pct.2	p_val_adj	gene	ident	method	ncells	significance
	<dbl>	<dbl>	<lgl>	<lgl>	<dbl>	<chr>	<chr>	<chr>	<int>	<chr>
1	0.04199363	-0.015279653	NA	NA	0.9916263	GNPDA2	X1	MAST.cov	22	>=0.05
2	0.04758570	0.133542942	NA	NA	0.9916263	RPS7P7	X1	MAST.cov	22	>=0.05
3	0.09462442	0.001029732	NA	NA	0.9916263	CHRNA9	X1	MAST.cov	22	>=0.05
4	0.10635680	0.012400904	NA	NA	0.9916263	KLHL5	X1	MAST.cov	22	>=0.05
5	0.11720622	NA	NA	NA	0.9916263	AC095057.3	X1	MAST.cov	22	>=0.05
6	0.12308059	-0.001536993	NA	NA	0.9916263	PHOX2B	X1	MAST.cov	22	>=0.05

head(genes.bed.detected)

A data.frame: 6 × 7

	chrom	start	stop	gene	score	strand	type
	<chr>	<dbl>	<dbl>	<chr>	<chr>	<chr>	<chr>
13	chr4	38772237	38782990	TLR10	.	-	gene
14	chr4	38790676	38856817	TLR1	.	-	gene
15	chr4	38823714	38856817	TLR6	.	-	gene
16	chr4	38867676	38945739	FAM114A1	.	+	gene
18	chr4	38966743	39032922	TMEM156	.	-	gene
19	chr4	39045038	39126857	KLHL5	.	+	gene

jumped_gene_counts <- c()
LFC <- c()
LFC_diff <- c()
for (i in 1:nrow(ghits.bedpe)){
    for (j in 1:nrow(genes.bed.detected)){
        if(genes.bed.detected$start[j]>=min(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & genes.bed.detected$stop[j]<=max(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & ghits.bedpe$gene[i]!=genes.bed.detected$gene[j]){
            LFC <- c(LFC, if(!is.na(as.numeric(TAP_DE$avg_logFC[which(TAP_DE$gene == genes.bed.detected$gene[j] & TAP_DE$ident == ghits.bedpe$gRNA[i])]))){as.numeric(TAP_DE$avg_logFC[which(TAP_DE$gene == genes.bed.detected$gene[j] & TAP_DE$ident == ghits.bedpe$gRNA[i])])})
        }
        if(j == nrow(genes.bed.detected)){
            LFC_diff <- c(LFC_diff, sum(ghits.bedpe$score[i]-LFC)/length(LFC))
            LFC <- c()
        }
   }
}

length(LFC_diff)

211

sum(is.na(LFC_diff))

67

ggplot(data.frame(LFC_diff), aes(x=LFC_diff)) + 
  geom_histogram()+theme_classic()+xlab("LFC (target genes vs. jumped genes)")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )

`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning message:
“Removed 67 rows containing non-finite values (`stat_bin()`).”

pdf("LFC_target_vs_jumped_202212.pdf",width=6,height=6)
ggplot(data.frame(LFC_diff), aes(x=LFC_diff)) + 
  geom_histogram()+theme_classic()+xlab("LFC (target genes vs. jumped genes)")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()

`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning message:
“Removed 67 rows containing non-finite values (`stat_bin()`).”

png: 2

hist(LFC_diff, main = "", xlab="LFC target genes vs. jumped genes", ylab="Counts", cex.lab=1.5, breaks=30)

ghits.bedpe$LFC_diff <- LFC_diff

options(repr.plot.width=8, repr.plot.height=8)
ggplot(ghits.bedpe, aes(LFC_diff, log_pvaladj))+ geom_point(size=4)+ theme_minimal() + xlab("LFC target genes vs. jumped genes") + ylab("-log adjusted p-value") + 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20))+
                                    theme_classic()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

Warning message:
“Removed 67 rows containing missing values (`geom_point()`).”

summary(ghits.bedpe$LFC_diff)

    Min.  1st Qu.   Median     Mean  3rd Qu.     Max.     NA's 
-1.02476 -0.04538  0.00420  0.06123  0.08660  1.36165       67 

options(repr.plot.width=8, repr.plot.height=8)
ggplot(ghits.bedpe, aes(distance.TSS, log_pvaladj)) +geom_point(size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Distance to TSS")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 20))+
labs(color="Fraction\nsignificant\ngRNAs")+
                                    theme_classic()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

options(repr.plot.width=16, repr.plot.height=8)

ggplot(ghits.bedpe, aes(distance.TSS, log_pvaladj,color=gene)) +geom_point()+
  geom_smooth(method=lm, se=FALSE, fullrange=FALSE)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Distance to TSS")+
                                    theme_classic()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

`geom_smooth()` using formula = 'y ~ x'

options(repr.plot.width=12, repr.plot.height=8)
ggplot(ghits.bedpe, aes(reorder(gene, distance.TSS, mean), distance.TSS/1000000)) + geom_boxplot() + theme_minimal()+ylab("Distance to TSS (Mb)")+
  theme(axis.title.x=element_blank(),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
                                    theme_classic()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,),axis.text.x = element_text(angle=60, hjust=1)
)

sort(table(ghits.bedpe$gRNA)[table(ghits.bedpe$gRNA)>1], decreasing = TRUE)

X770 X808 X185 X512  X58 X829 X886 X124 X214 X283 X341 X350 X356 X380 X404 X572 
   5    5    3    3    3    3    3    2    2    2    2    2    2    2    2    2 
X624 X634 X651 X698 X717  X74 X780 X854 X882 X893 X936 X942 
   2    2    2    2    2    2    2    2    2    2    2    2 

names(table(ghits.bedpe$gRNA)[table(ghits.bedpe$gRNA)>1])

1. 'X124'
2. 'X185'
3. 'X214'
4. 'X283'
5. 'X341'
6. 'X350'
7. 'X356'
8. 'X380'
9. 'X404'
10. 'X512'
11. 'X572'
12. 'X58'
13. 'X624'
14. 'X634'
15. 'X651'
16. 'X698'
17. 'X717'
18. 'X74'
19. 'X770'
20. 'X780'
21. 'X808'
22. 'X829'
23. 'X854'
24. 'X882'
25. 'X886'
26. 'X893'
27. 'X936'
28. 'X942'

ghits.bedpe <- ghits.bedpe %>% filter(gRNA %in% names(table(ghits.bedpe$gRNA)[table(ghits.bedpe$gRNA)>1]))

ghits.up.bedpe <- ghits.bedpe[which(ghits.bedpe$score>0),]
ghits.down.bedpe <- ghits.bedpe[which(ghits.bedpe$score<0),] 
ghits.down.bedpe$score <- abs(ghits.down.bedpe$score)
genes.up.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.up.bedpe$name))))), genes.bed$gene),]
genes.down.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.down.bedpe$name))))), genes.bed$gene),]
genes.up.bed <- rbind(genes.up.bed, genes.down.bed)
genes.up.bed <- genes.up.bed %>% distinct() %>% arrange(gene)
gRNA.up.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.up.bedpe$name))))), gRNA.bed$gene),]
gRNA.down.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.down.bedpe$name))))), gRNA.bed$gene),]
gRNA.up.bed <- rbind(gRNA.up.bed, gRNA.down.bed)
gRNA.up.bed <- gRNA.up.bed %>% distinct()%>% arrange(gene)

nb.cols <- length(table(c(ghits.up.bedpe$samplenumber,ghits.down.bedpe$samplenumber)))
chrom = "chr4"
chromstart = 38500000
chromend = 44500000

#Type
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 0, 4))
pbpe = plotBedpe(ghits.bedpe,chrom,chromstart,chromend,plottype="lines",
colorby=as.numeric(as.factor(ghits.bedpe$type)),
colorbycol=SushiColors(2),flip=TRUE)
legend("right",inset = 0.1,cex=1,text.width=2,legend=names(table(as.character(as.factor(ghits.bedpe$type)))),
col=SushiColors(2)(2),pch=19,bty='n',text.font=2,y.intersp=2)
axis(side=2,labels = FALSE, tick = FALSE)
mtext("regulation",side=2,line=3,cex=1,font=2)
#Log_FoldChange
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
heights = ghits.bedpe$score,plottype="loops",
colorby=ghits.bedpe$samplenumber,
colorbycol=colorRampPalette(rev(brewer.pal(nb.cols,"Paired"))),flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("avg_logFC",side=2,line=3,cex=1,font=2)
#GeneTrack
options(repr.plot.width=16, repr.plot.height=2.5)
par(mar = c(0, 4, 0, 4))
pg = suppressWarnings(plotGenes(genes.up.bed,chrom,chromstart,chromend ,
types=genes.up.bed$type,maxrows=10,bheight=0.1,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.4,fontsize=0.8,arrowlength = 0.025,
labeltext=TRUE, col=colorRampPalette(rev(brewer.pal(nb.cols,"Paired")))(nb.cols)))
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gene",side=2,line=3,cex=1,font=2)
#gRNATRACK
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(0, 4, 0, 4))
pg = plotGenes(gRNA.up.bed,chrom,chromstart,chromend ,
types=gRNA.up.bed$type,maxrows=50,bheight=0,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.2,fontsize=0.8,arrowlength = 0.01,
labeltext=TRUE, col=c())
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gRNA",side=2,line=3,cex=1,font=2)

[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"

[1] "yes"

[1] "yes"

ghits.bedpe$distance.TSS <- apply(ghits.bedpe, 1, function(x){if(x[9]=="+"&x[10]=="+"){abs(as.numeric(x[2])-as.numeric(x[5]))}else if(x[9]=="+"&x[10]=="-"){abs(as.numeric(x[2])-as.numeric(x[6]))}else if(x[9]=="-"&x[10]=="+"){abs(as.numeric(x[3])-as.numeric(x[5]))}else{abs(as.numeric(x[3])-as.numeric(x[6]))}})

options(repr.plot.width=16, repr.plot.height=8)

ggplot(ghits.bedpe, aes(distance.TSS, log_pvaladj,color=gene)) +geom_point()+
  geom_smooth(method=lm, se=FALSE, fullrange=FALSE)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Distance to TSS")

`geom_smooth()` using formula = 'y ~ x'

options(repr.plot.width=12, repr.plot.height=8)
ggplot(ghits.bedpe, aes(reorder(gene, distance.TSS, mean), distance.TSS/1000000)) + geom_boxplot() + theme_minimal()+ylab("Distance to TSS (Mb)")+
  theme(axis.title.x=element_blank(),axis.text.x = element_text(angle=60, colour="black", hjust=1, size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))+
                                    theme_classic()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,),axis.text.x = element_text(angle=60, hjust=1)
)

ghits.bedpe <- ghits.bedpe %>% filter(gRNA %in% names(table(ghits.bedpe$gRNA)[table(ghits.bedpe$gRNA)>1]))

ghits.up.bedpe <- ghits.bedpe[which(ghits.bedpe$score>0),]
ghits.down.bedpe <- ghits.bedpe[which(ghits.bedpe$score<0),] 
ghits.down.bedpe$score <- abs(ghits.down.bedpe$score)
genes.up.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.up.bedpe$name))))), genes.bed$gene),]
genes.down.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.down.bedpe$name))))), genes.bed$gene),]
genes.up.bed <- rbind(genes.up.bed, genes.down.bed)
genes.up.bed <- genes.up.bed %>% distinct() %>% arrange(gene)
gRNA.up.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.up.bedpe$name))))), gRNA.bed$gene),]
gRNA.down.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.down.bedpe$name))))), gRNA.bed$gene),]
gRNA.up.bed <- rbind(gRNA.up.bed, gRNA.down.bed)
gRNA.up.bed <- gRNA.up.bed %>% distinct()
gRNA.up.bed$gene <- gsub("PHOX2B.","B",gRNA.up.bed$gene)

nb.cols <- length(table(c(ghits.up.bedpe$samplenumber,ghits.down.bedpe$samplenumber)))
chrom = "chr4"
chromstart = 38500000
chromend = 44500000

options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 0, 4))
pbpe = plotBedpe(ghits.bedpe,chrom,chromstart,chromend,plottype="lines",
colorby=as.numeric(as.factor(ghits.bedpe$type)),
colorbycol=SushiColors(2),flip=TRUE)
legend("right",inset = 0.1,cex=1,text.width=2,legend=names(table(as.character(as.factor(ghits.bedpe$type)))),
col=SushiColors(2)(2),pch=19,bty='n',text.font=2,y.intersp=2)
axis(side=2,labels = FALSE, tick = FALSE)
mtext("regulation",side=2,line=3,cex=1,font=2)
#Log_FoldChange
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
heights = ghits.bedpe$score,plottype="loops",
colorby=ghits.bedpe$samplenumber,
colorbycol=colorRampPalette(rev(brewer.pal(12,"Paired"))),flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("avg_logFC",side=2,line=3,cex=1,font=2)
#GeneTrack
options(repr.plot.width=16, repr.plot.height=2.5)
par(mar = c(0, 4, 0, 4))
pg = suppressWarnings(plotGenes(genes.up.bed,chrom,chromstart,chromend ,
types=genes.up.bed$type,maxrows=10,bheight=0.1,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.4,fontsize=0.8,arrowlength = 0.025,
labeltext=TRUE, col=colorRampPalette(rev(brewer.pal(12,"Paired")))(nb.cols)))
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gene",side=2,line=3,cex=1,font=2)
#gRNATRACK
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(0, 4, 0, 4))
pg = plotGenes(gRNA.up.bed,chrom,chromstart,chromend ,
types=gRNA.up.bed$type,maxrows=50,bheight=0,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.2,fontsize=0.8,arrowlength = 0.01,
labeltext=TRUE, col=c())
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gRNA",side=2,line=3,cex=1,font=2)

[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"

[1] "yes"

[1] "yes"

From here region

ghits <- TAP_DE[grep("^Region", TAP_DE$ident),]

chrom1 <- br_anno$Chr[match(ghits$ident, br_anno$Region_name)]
start1 <- br_anno$Region_start[match(ghits$ident, br_anno$Region_name)]
end1 <- br_anno$Region_end[match(ghits$ident, br_anno$Region_name)]
chrom2 <- genes.bed$chrom[match(ghits$gene, genes.bed$gene)]
start2 <- genes.bed$start[match(ghits$gene, genes.bed$gene)]
end2 <- genes.bed$stop[match(ghits$gene, genes.bed$gene)]
ghits$ident <- gsub("^Region_","R",ghits$ident)
name <- paste0(ghits$ident,"_",ghits$gene)
ghits$ident <- gsub("^R","Region_",ghits$ident)
score <- ghits$avg_logFC
strand1 <- br_anno$strand[match(ghits$ident, br_anno$Region_name)]
strand2 <- genes.bed$strand[match(ghits$gene, genes.bed$gene)]
samplenumber <- as.numeric(as.factor(ghits$gene))
gene <- ghits$gene
gRNA <- ghits$ident
log_pvaladj <- -log(ghits$p_val_adj)
type <- ghits$avg_logFC
type[which(type > 0)] <- "up_regulated"
type[which(type < 0)] <- "down_regulated"
#avg_logFC <- ghits$avg_logFC
br_anno$Region_name <- gsub("^Region_","R",br_anno$Region_name)
gRNA.bed <- data.frame(chrom=br_anno$Chr, start=br_anno$Region_start, stop=br_anno$Region_end, gene=br_anno$Region_name, score=".", strand=br_anno$strand, type="gene")
gRNA.bed <- gRNA.bed[!is.na(gRNA.bed$gene),]
gRNA.bed <- gRNA.bed %>% distinct()
#ALL
ghits.bedpe <- data.frame(chrom1, start1, end1, chrom2, start2, end2, name, score, strand1, strand2, samplenumber, gene, gRNA, log_pvaladj, type)
ghits.bedpe <- ghits.bedpe[!is.na(ghits.bedpe$score),]
ghits.bedpe$samplenumber <- as.numeric(as.factor(ghits.bedpe$gene))
ghits.up.bedpe <- ghits.bedpe[which(ghits.bedpe$score>0),]
ghits.down.bedpe <- ghits.bedpe[which(ghits.bedpe$score<0),] 
ghits.down.bedpe$score <- abs(ghits.down.bedpe$score)
genes.up.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.up.bedpe$name))))), genes.bed$gene),]
genes.down.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.down.bedpe$name))))), genes.bed$gene),]
genes.up.bed <- rbind(genes.up.bed, genes.down.bed)
genes.up.bed <- genes.up.bed %>% distinct() %>% arrange(gene)
gRNA.up.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.up.bedpe$name))))), gRNA.bed$gene),]
gRNA.down.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.down.bedpe$name))))), gRNA.bed$gene),]
gRNA.up.bed <- rbind(gRNA.up.bed, gRNA.down.bed)
gRNA.up.bed <- gRNA.up.bed %>% distinct()
br_anno$Region_name <- gsub("^R","Region_",br_anno$Region_name)

## For region
#ghits.bedpe <- TAP_DE.bedpe[grep("^Region", TAP_DE.bedpe$gRNA),]
#ghits.bedpe <- ghits.bedpe[!is.na(ghits.bedpe$chrom1),]

#My definition of linear distance
#ghits.bedpe$distance.TSS <- apply(ghits.bedpe, 1, function(x){if(x[9]=="+"&x[10]=="+"){abs(as.numeric(x[2])-as.numeric(x[5]))}else if(x[9]=="+"&x[10]=="-"){abs(as.numeric(x[2])-as.numeric(x[6]))}else if(x[9]=="-"&x[10]=="+"){abs(as.numeric(x[3])-as.numeric(x[5]))}else{abs(as.numeric(x[3])-as.numeric(x[6]))}})

##Scott's linear distance, always started from start site
ghits.bedpe$distance.TSS <- apply(ghits.bedpe, 1, function(x){abs(as.numeric(x[2])-as.numeric(x[5]))})
ghits.bedpe$significance <- rep("adj.pval >= 0.05", nrow(ghits.bedpe))
ghits.bedpe$significance[ghits.bedpe$log_pvaladj>1.3] <- "adj.pval < 0.05"

options(repr.plot.width=8, repr.plot.height=8)
ggplot(ghits.bedpe, aes(distance.TSS/1000000, log_pvaladj)) +geom_point(aes(colour = significance),size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Distance to TSS (Mb)")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
labs(color="Region")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

ghits.bedpe <- ghits.bedpe %>% filter(significance=="adj.pval < 0.05")

summary(ghits.bedpe$distance.TSS)

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
     97  195534 1258251 1356463 2265607 3942865 

pdf("Distance_to_TSS_vs_pvalue_region_202212.pdf",width=8,height=6)
ggplot(ghits.bedpe, aes(distance.TSS/1000000, log_pvaladj)) +geom_point(aes(colour = significance),size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Distance to TSS (Mb)")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
labs(color="Region")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()

png: 2

ghits <- rhits

colnames(br_anno)

1. 'Region_name'
2. 'Region_pvalue'
3. 'Region_fdr'
4. 'Region_slope'
5. 'Chr'
6. 'Region_start'
7. 'Region_end'
8. 'Bins_in_region'
9. 'Bin'
10. 'Bin_slope'
11. 'Bin_pvalue'
12. 'Bin_fdr'
13. 'Bin_speed'
14. 'Bin_start'
15. 'Bin_end'
16. 'guide_start'
17. 'guide_end'
18. 'strand'
19. 'guide_sequence'
20. 'guide_replicate'
21. 'guide_name'
22. 'guide_logfold'
23. 'guide_pvalue'
24. 'giude_classification'
25. 'guide_fdr'
26. 'Rhapsody_name'
27. 'class'

chrom1 <- br_anno$Chr[match(ghits$ident, br_anno$Region_name)]
start1 <- br_anno$Region_start[match(ghits$ident, br_anno$Region_name)]
end1 <- br_anno$Region_end[match(ghits$ident, br_anno$Region_name)]
chrom2 <- genes.bed$chrom[match(ghits$gene, genes.bed$gene)]
start2 <- genes.bed$start[match(ghits$gene, genes.bed$gene)]
end2 <- genes.bed$stop[match(ghits$gene, genes.bed$gene)]
ghits$ident <- gsub("^Region_","R",ghits$ident)
name <- paste0(ghits$ident,"_",ghits$gene)
ghits$ident <- gsub("^R","Region_",ghits$ident)
score <- ghits$avg_logFC
strand1 <- br_anno$strand[match(ghits$ident, br_anno$Region_name)]
strand2 <- genes.bed$strand[match(ghits$gene, genes.bed$gene)]
samplenumber <- as.numeric(as.factor(ghits$gene))
gene <- ghits$gene
gRNA <- ghits$ident
log_pvaladj <- -log(ghits$p_val_adj)
type <- ghits$avg_logFC
type[which(type > 0)] <- "up_regulated"
type[which(type < 0)] <- "down_regulated"
br_anno$Region_name <- gsub("^Region_","R",br_anno$Region_name)
gRNA.bed <- data.frame(chrom=br_anno$Chr, start=br_anno$Region_start, stop=br_anno$Region_end, gene=br_anno$Region_name, score=".", strand=br_anno$strand, type="gene")
gRNA.bed <- gRNA.bed[!is.na(gRNA.bed$gene),]
gRNA.bed <- gRNA.bed %>% distinct()
#ALL
ghits.bedpe <- data.frame(chrom1, start1, end1, chrom2, start2, end2, name, score, strand1, strand2, samplenumber, gene, gRNA, log_pvaladj, type)
ghits.bedpe <- ghits.bedpe[!is.na(ghits.bedpe$score),]
ghits.bedpe$samplenumber <- as.numeric(as.factor(ghits.bedpe$gene))
ghits.up.bedpe <- ghits.bedpe[which(ghits.bedpe$score>0),]
ghits.down.bedpe <- ghits.bedpe[which(ghits.bedpe$score<0),] 
ghits.down.bedpe$score <- abs(ghits.down.bedpe$score)
genes.up.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.up.bedpe$name))))), genes.bed$gene),]
genes.down.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.down.bedpe$name))))), genes.bed$gene),]
genes.up.bed <- rbind(genes.up.bed, genes.down.bed)
genes.up.bed <- genes.up.bed %>% distinct() %>% arrange(gene)
gRNA.up.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.up.bedpe$name))))), gRNA.bed$gene),]
gRNA.down.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.down.bedpe$name))))), gRNA.bed$gene),]
gRNA.up.bed <- rbind(gRNA.up.bed, gRNA.down.bed)
gRNA.up.bed <- gRNA.up.bed %>% distinct()
br_anno$Region_name <- gsub("^R","Region_",br_anno$Region_name)

head(ghits.bedpe)

A data.frame: 6 x 15

	chrom1	start1	end1	chrom2	start2	end2	name	score	strand1	strand2	samplenumber	gene	gRNA	log_pvaladj	type
	<chr>	<int>	<int>	<chr>	<dbl>	<dbl>	<chr>	<dbl>	<chr>	<chr>	<dbl>	<chr>	<chr>	<dbl>	<chr>
1	chr4	40749315	40752221	chr4	40423266	40630875	R1_RBM47	0.0001855366	+	-	22	RBM47	Region_1	4.697194	up_regulated
2	chr4	40749315	40752221	chr4	40749924	40811184	R1_NSUN7	0.0049871483	+	+	18	NSUN7	Region_1	3.452971	up_regulated
3	chr4	40749315	40752221	chr4	42471809	42472380	R1_RPS7P7	0.1037766838	+	+	23	RPS7P7	Region_1	3.452971	up_regulated
4	chr4	41012671	41016125	chr4	40020239	40021517	R132_KRT18P25	0.0243873463	+	+	13	KRT18P25	Region_132	12.467571	up_regulated
5	chr4	41012671	41016125	chr4	44693945	44694386	R132_AC096586.2	-0.0003783229	+	-	3	AC096586.2	Region_132	3.386169	down_regulated
6	chr4	41050311	41051029	chr4	43898961	43899351	R152_NDUFB4P12	0.2486232951	+	+	17	NDUFB4P12	Region_152	4.827161	up_regulated

#meta <- read.table("../../CW_data/Dusa/lastForCheWei.tsv", sep="\t", head=TRUE)
#meta$ident <- gsub("egion_","",meta$ident)
#meta <- meta %>% mutate(name = paste0(ident,"_",gene))
#ghits.bedpe <- left_join(ghits.bedpe, meta, by = "name")
#ghits.bedpe[is.na(ghits.bedpe)] <- 0

#head(ghits.bedpe)

A data.frame: 6 x 53

	chrom1	start1	end1	chrom2	start2	end2	name	score	strand1	strand2	...	maxAbcScore	regionH3K27ac	geneH3K27ac	regionH3K4me1	geneH3K4me1	regionAtac	geneAtac	regionH3K4me3	geneH3K4me3	gc
	<chr>	<int>	<int>	<chr>	<dbl>	<dbl>	<chr>	<dbl>	<chr>	<chr>	...	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>
1	chr4	40749315	40752221	chr4	40423266	40630875	R1_RBM47	0.0001855366	+	-	...	0.055817	125.748503	3.992016	43.912176	5.988024	238.52295	50.89820	254.491018	3.992016	0.523400
2	chr4	40749315	40752221	chr4	40749924	40811184	R1_NSUN7	0.0049871483	+	+	...	0.293307	125.748503	249.500998	43.912176	24.950100	238.52295	434.13174	254.491018	392.215569	0.523400
3	chr4	40749315	40752221	chr4	42471809	42472380	R1_RPS7P7	0.1037766838	+	+	...	0.000000	125.748503	1.996008	43.912176	2.994012	238.52295	21.95609	254.491018	2.994012	0.523400
4	chr4	41012671	41016125	chr4	40020239	40021517	R132_KRT18P25	0.0243873463	+	+	...	0.000000	0.000000	0.000000	1.996008	0.000000	22.95409	18.96208	0.000000	3.992016	0.403301
5	chr4	41012671	41016125	chr4	44693945	44694386	R132_AC096586.2	-0.0003783229	+	-	...	0.000000	0.000000	0.000000	1.996008	2.994012	22.95409	32.93413	0.000000	4.990020	0.403301
6	chr4	41050311	41051029	chr4	43898961	43899351	R152_NDUFB4P12	0.2486232951	+	+	...	0.000000	1.996008	8.982036	6.986028	2.994012	29.94012	10.97804	3.992016	1.996008	0.452646

colnames(ghits.bedpe)

1. 'chrom1'
2. 'start1'
3. 'end1'
4. 'chrom2'
5. 'start2'
6. 'end2'
7. 'name'
8. 'score'
9. 'strand1'
10. 'strand2'
11. 'samplenumber'
12. 'gene.x'
13. 'gRNA'
14. 'log_pvaladj'
15. 'type'
16. 'p_val'
17. 'avg_logFC'
18. 'pct.1'
19. 'pct.2'
20. 'p_val_adj'
21. 'gene.y'
22. 'ident'
23. 'method'
24. 'ncells'
25. 'pairId'
26. 'regionChr'
27. 'regionStart'
28. 'regionEnd'
29. 'geneTssChr'
30. 'geneTssStart'
31. 'geneTssEnd'
32. 'width'
33. 'class'
34. 'tissue'
35. 'bulkPromHit'
36. 'sig'
37. 'dist'
38. 'hicScore'
39. 'hicInteracts'
40. 'maxCapcScore'
41. 'capcInteracts'
42. 'interacts'
43. 'maxEpiMapLinkScore'
44. 'maxAbcScore'
45. 'regionH3K27ac'
46. 'geneH3K27ac'
47. 'regionH3K4me1'
48. 'geneH3K4me1'
49. 'regionAtac'
50. 'geneAtac'
51. 'regionH3K4me3'
52. 'geneH3K4me3'
53. 'gc'

ghits.bedpe$gene.x

1. 'RBM47'
2. 'NSUN7'
3. 'RPS7P7'
4. 'KRT18P25'
5. 'AC096586.2'
6. 'NDUFB4P12'
7. 'NDUFB4P12'
8. 'APBB2'
9. 'TLR1'
10. 'LINC02265'
11. 'KRT18P25'
12. 'APBB2'
13. 'CHRNA9'
14. 'PDS5A'
15. 'TLR1'
16. 'N4BP2'
17. 'LINC00682'
18. 'KRT18P25'
19. 'GNPDA2'
20. 'RPS7P7'
21. 'PHOX2B'
22. 'PHOX2B'
23. 'SLC30A9'
24. 'ARL4AP2'
25. 'PHOX2B'
26. 'PHOX2B'
27. 'APBB2'
28. 'PHOX2B'
29. 'PABPC1P1'
30. 'PHOX2B'
31. 'LINC00682'
32. 'PHOX2B'
33. 'LINC00682'
34. 'PHOX2B'
35. 'LINC00682'
36. 'PHOX2B'
37. 'PHOX2B'
38. 'PHOX2B'
39. 'LINC00682'
40. 'PHOX2B'
41. 'RPS7P7'
42. 'AC095057.3'
43. 'SLC30A9'
44. 'TLR1'
45. 'AC096586.1'
46. 'TMEM33'
47. 'AC105389.1'
48. 'LINC02265'
49. 'CHRNA9'
50. 'CHRNA9'
51. 'BEND4'
52. 'BEND4'
53. 'AC098590.1'
54. 'CHRNA9'
55. 'NSUN7'
56. 'LINC02265'
57. 'SHISA3'
58. 'ZBTB12BP'
59. 'BEND4'
60. 'SHISA3'
61. 'SHISA3'
62. 'SHISA3'
63. 'BEND4'
64. 'SHISA3'
65. 'RPS7P7'
66. 'SHISA3'
67. 'SHISA3'
68. 'SHISA3'
69. 'TLR6'
70. 'UGDH'
71. 'SHISA3'
72. 'SHISA3'
73. 'TMEM156'
74. 'PABPC1P1'
75. 'SHISA3'
76. 'ARL4AP2'
77. 'RPS7P7'
78. 'ATP8A1'
79. 'SHISA3'
80. 'TLR6'
81. 'LINC02265'
82. 'SHISA3'
83. 'SHISA3'
84. 'ATP8A1'
85. 'SHISA3'
86. 'AC096734.2'
87. 'ATP8A1'
88. 'WDR19'
89. 'GNPDA2'
90. 'PHOX2B'
91. 'TMEM156'

ghits.bedpe$gene.y

1. 'RBM47'
2. 'NSUN7'
3. 'RPS7P7'
4. 'KRT18P25'
5. 'AC096586.2'
6. 'NDUFB4P12'
7. 'NDUFB4P12'
8. 'APBB2'
9. 'TLR1'
10. 'LINC02265'
11. 'KRT18P25'
12. 'APBB2'
13. 'CHRNA9'
14. 'PDS5A'
15. 'TLR1'
16. 'N4BP2'
17. 'LINC00682'
18. 'KRT18P25'
19. 'GNPDA2'
20. 'RPS7P7'
21. 'PHOX2B'
22. 'PHOX2B'
23. 'SLC30A9'
24. 'ARL4AP2'
25. 'PHOX2B'
26. 'PHOX2B'
27. 'APBB2'
28. 'PHOX2B'
29. 'PABPC1P1'
30. 'PHOX2B'
31. 'LINC00682'
32. 'PHOX2B'
33. 'LINC00682'
34. 'PHOX2B'
35. 'LINC00682'
36. 'PHOX2B'
37. 'PHOX2B'
38. 'PHOX2B'
39. 'LINC00682'
40. 'PHOX2B'
41. 'RPS7P7'
42. 'AC095057.3'
43. 'SLC30A9'
44. 'TLR1'
45. 'AC096586.1'
46. 'TMEM33'
47. 'AC105389.1'
48. 'LINC02265'
49. 'CHRNA9'
50. 'CHRNA9'
51. 'BEND4'
52. 'BEND4'
53. 'AC098590.1'
54. 'CHRNA9'
55. 'NSUN7'
56. 'LINC02265'
57. 'SHISA3'
58. 'ZBTB12BP'
59. 'BEND4'
60. 'SHISA3'
61. 'SHISA3'
62. 'SHISA3'
63. 'BEND4'
64. 'SHISA3'
65. 'RPS7P7'
66. 'SHISA3'
67. 'SHISA3'
68. 'SHISA3'
69. 'TLR6'
70. 'UGDH'
71. 'SHISA3'
72. 'SHISA3'
73. 'TMEM156'
74. 'PABPC1P1'
75. 'SHISA3'
76. 'ARL4AP2'
77. 'RPS7P7'
78. 'ATP8A1'
79. 'SHISA3'
80. 'TLR6'
81. 'LINC02265'
82. 'SHISA3'
83. 'SHISA3'
84. 'ATP8A1'
85. 'SHISA3'
86. 'AC096734.2'
87. 'ATP8A1'
88. 'WDR19'
89. 'GNPDA2'
90. 'PHOX2B'
91. 'TMEM156'

nb.cols <- length(table(c(ghits.up.bedpe$samplenumber,ghits.down.bedpe$samplenumber)))
chrom = "chr4"
chromstart = 38500000
chromend = 44500000

#Type
pdf("track_regulation_region_202212.pdf",width=16,height=2)
options(repr.plot.width=16, repr.plot.height=4)
par(mar = c(2, 4, 0, 4))
pbpe = plotBedpe(ghits.bedpe,chrom,chromstart,chromend,plottype="lines",
colorby=as.numeric(as.factor(ghits.bedpe$type)),
colorbycol=SushiColors(2),flip=TRUE)
legend("right",inset = 0.1,cex=1,text.width=2,legend=names(table(as.character(as.factor(ghits.bedpe$type)))),
col=SushiColors(2)(2),pch=19,bty='n',text.font=2,y.intersp=2)
axis(side=2,labels = FALSE, tick = FALSE)
mtext("regulation",side=2,line=3,cex=1,font=2)
dev.off()

#Log_FoldChange
pdf("track_avg_logFC_region_202212.pdf",width=16,height=2)
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
heights = ghits.bedpe$score,plottype="loops",
colorby=ghits.bedpe$samplenumber,
colorbycol=colorRampPalette(rev(brewer.pal(nb.cols,"Paired"))),flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("avg_logFC",side=2,line=3,cex=1,font=2)
dev.off()

#Hi-C
pdf("track_Hi-C_region_202212.pdf",width=16,height=2)
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
heights = ghits.bedpe$hicScore,plottype="loops",
colorby=ghits.bedpe$samplenumber,
colorbycol=colorRampPalette(rev(brewer.pal(12,"Paired"))),flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("Hi-C",side=2,line=3,cex=1,font=2)
dev.off()

#CaptureC
pdf("track_CaptureC_region_202212.pdf",width=16,height=2)
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
heights = ghits.bedpe$maxCapcScore,plottype="loops",
colorby=ghits.bedpe$samplenumber,
colorbycol=colorRampPalette(rev(brewer.pal(12,"Paired"))),flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("CaptureC",side=2,line=3,cex=1,font=2)
dev.off()

#GeneTrack
pdf("track_gene_region_202212.pdf",width=16,height=1.5)
options(repr.plot.width=16, repr.plot.height=1.5)
par(mar = c(0, 4, 0, 4))
pg = suppressWarnings(plotGenes(genes.up.bed,chrom,chromstart,chromend ,
types=genes.up.bed$type,maxrows=10,bheight=0.1,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.4,fontsize=0.8,arrowlength = 0.025,
labeltext=TRUE, col=colorRampPalette(rev(brewer.pal(nb.cols,"Paired")))(nb.cols)))
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gene",side=2,line=3,cex=1,font=2)
dev.off()

#gRNATRACK
pdf("track_region_region_202212.pdf",width=16,height=3)
options(repr.plot.width=16, repr.plot.height=8)
par(mar = c(0, 4, 0, 4))
pg = plotGenes(gRNA.up.bed,chrom,chromstart,chromend ,
types=gRNA.up.bed$type,maxrows=50,bheight=0,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.2,fontsize=0.8,arrowlength = 0.01,
labeltext=TRUE, col=c())
axis(side=2,labels = FALSE, tick = FALSE)
mtext("region",side=2,line=3,cex=1,font=2)
dev.off()

[1] "yes"
[1] "yes"

png: 2

[1] "yes"
[1] "yes"

png: 2

[1] "yes"
[1] "yes"

png: 2

[1] "yes"
[1] "yes"

png: 2

[1] "yes"

png: 2

[1] "yes"

png: 2

options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 0, 4))
pbpe = plotBedpe(ghits.bedpe,chrom,chromstart,chromend,plottype="lines",
colorby=as.numeric(as.factor(ghits.bedpe$type)),
colorbycol=SushiColors(2),flip=TRUE)
legend("right",inset = 0.1,cex=1,text.width=2,legend=names(table(as.character(as.factor(ghits.bedpe$type)))),
col=SushiColors(2)(2),pch=19,bty='n',text.font=2,y.intersp=4)
axis(side=2,labels = FALSE, tick = FALSE)
mtext("regulation",side=2,line=3,cex=1,font=2)
#Log_FoldChange
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
heights = ghits.bedpe$score,plottype="loops",
colorby=ghits.bedpe$samplenumber,
colorbycol=colorRampPalette(rev(brewer.pal(12,"Paired"))),flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("avg_logFC",side=2,line=3,cex=1,font=2)
#Hi-C
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
heights = ghits.bedpe$hicScore,plottype="loops",
colorby=ghits.bedpe$samplenumber,
colorbycol=colorRampPalette(rev(brewer.pal(12,"Paired"))),flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("Hi-C",side=2,line=3,cex=1,font=2)
#CaptureC
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe,chrom,chromstart,chromend,
heights = ghits.bedpe$maxCapcScore,plottype="loops",
colorby=ghits.bedpe$samplenumber,
colorbycol=colorRampPalette(rev(brewer.pal(12,"Paired"))),flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("CaptureC",side=2,line=3,cex=1,font=2)
#GeneTrack
options(repr.plot.width=16, repr.plot.height=1.5)
par(mar = c(0, 4, 0, 4))
pg = suppressWarnings(plotGenes(genes.up.bed,chrom,chromstart,chromend ,
types=genes.up.bed$type,maxrows=10,bheight=0.1,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.4,fontsize=0.8,arrowlength = 0.025,
labeltext=TRUE, col=colorRampPalette(rev(brewer.pal(12,"Paired")))(nb.cols)))
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gene",side=2,line=3,cex=1,font=2)
#gRNATRACK
options(repr.plot.width=16, repr.plot.height=3)
par(mar = c(0, 4, 0, 4))
pg = plotGenes(gRNA.up.bed,chrom,chromstart,chromend ,
types=gRNA.up.bed$type,maxrows=50,bheight=0,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.2,fontsize=0.8,arrowlength = 0.01,
labeltext=TRUE, col=c())
axis(side=2,labels = FALSE, tick = FALSE)
mtext("region",side=2,line=3,cex=1,font=2)

[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"

[1] "yes"
[1] "yes"

[1] "yes"
[1] "yes"

[1] "yes"

[1] "yes"

ghits.bedpe.PHOX2B <- ghits.bedpe %>% filter(gene.x == "PHOX2B")

head(ghits.bedpe.PHOX2B)

A data.frame: 6 x 53

	chrom1	start1	end1	chrom2	start2	end2	name	score	strand1	strand2	...	maxAbcScore	regionH3K27ac	geneH3K27ac	regionH3K4me1	geneH3K4me1	regionAtac	geneAtac	regionH3K4me3	geneH3K4me3	gc
	<chr>	<int>	<int>	<chr>	<dbl>	<dbl>	<chr>	<dbl>	<chr>	<chr>	...	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>
1	chr4	41713630	41714666	chr4	41744081	41748725	R477_PHOX2B	0.4677258	+	-	...	0.000000	38.922156	441.1178	24.950100	11.97605	52.89421	753.493	0.998004	431.1377	0.383205
2	chr4	41748711	41752752	chr4	41744081	41748725	R494_PHOX2B	-0.5493911	+	-	...	0.206476	639.720559	441.1178	49.900200	11.97605	252.49501	753.493	78.842315	431.1377	0.493195
3	chr4	41771129	41772268	chr4	41744081	41748725	R504_PHOX2B	0.3603152	+	-	...	0.000000	0.998004	441.1178	0.998004	11.97605	35.92814	753.493	2.994012	431.1377	0.399473
4	chr4	41784417	41785468	chr4	41744081	41748725	R512_PHOX2B	-0.3404573	+	-	...	0.019211	430.139721	441.1178	140.718563	11.97605	788.42315	753.493	7.984032	431.1377	0.426261
5	chr4	41795892	41798240	chr4	41744081	41748725	R520_PHOX2B	0.4048890	+	-	...	0.085094	114.770459	441.1178	145.708583	11.97605	105.78842	753.493	4.990020	431.1377	0.445486
6	chr4	41813778	41822745	chr4	41744081	41748725	R530_PHOX2B	-0.3854239	+	-	...	0.000000	20.958084	441.1178	25.948104	11.97605	55.88822	753.493	0.998004	431.1377	0.432140

chrom = "chr4"
chromstart = 41600000
chromend = 41900000

#Log_FoldChange
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe.PHOX2B,chrom,chromstart,chromend,
heights = ghits.bedpe.PHOX2B$score,plottype="loops",flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("avg_logFC",side=2,line=3,cex=1,font=2)
#Hi-C
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe.PHOX2B,chrom,chromstart,chromend,
heights = ghits.bedpe.PHOX2B$hicScore,plottype="loops",flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("Hi-C",side=2,line=3,cex=1,font=2)
#CaptureC
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe.PHOX2B,chrom,chromstart,chromend,
heights = ghits.bedpe.PHOX2B$maxCapcScore,plottype="loops",flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("CaptureC",side=2,line=3,cex=1,font=2)
#GeneTrack
options(repr.plot.width=16, repr.plot.height=1.5)
par(mar = c(0, 4, 0, 4))
pg = suppressWarnings(plotGenes(genes.up.bed,chrom,chromstart,chromend ,
types=genes.up.bed$type,maxrows=10,bheight=0.1,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.4,fontsize=0.8,arrowlength = 0.025,
labeltext=TRUE, col=colorRampPalette(rev(brewer.pal(12,"Paired")))(nb.cols)))
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gene",side=2,line=3,cex=1,font=2)

[1] "yes"
[1] "yes"
[1] "yes"
[1] "yes"

[1] "yes"
[1] "yes"

[1] "yes"

pdf("PHOX2B_track_avg_logFC_region_202212.pdf",width=16,height=2)
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe.PHOX2B,chrom,chromstart,chromend,
heights = ghits.bedpe.PHOX2B$score,plottype="loops",flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("avg_logFC",side=2,line=3,cex=1,font=2)
dev.off()
pdf("PHOX2B_track_Hi-C_region_202212.pdf",width=16,height=2)
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe.PHOX2B,chrom,chromstart,chromend,
heights = ghits.bedpe.PHOX2B$hicScore,plottype="loops",flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("Hi-C",side=2,line=3,cex=1,font=2)
dev.off()
pdf("PHOX2B_track_CaptureC_region_202212.pdf",width=16,height=2)
options(repr.plot.width=16, repr.plot.height=2)
par(mar = c(2, 4, 2, 4))
pbpe = suppressWarnings(plotBedpe(ghits.bedpe.PHOX2B,chrom,chromstart,chromend,
heights = ghits.bedpe.PHOX2B$maxCapcScore,plottype="loops",flip=FALSE))
#lwdby=ghits.bedpe$log_pvaladj
labelgenome( chrom, chromstart,chromend,n=10,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("CaptureC",side=2,line=3,cex=1,font=2)
dev.off()
pdf("PHOX2B_track_gene_region_202212.pdf",width=16,height=1.5)
options(repr.plot.width=16, repr.plot.height=1.5)
par(mar = c(0, 4, 0, 4))
pg = suppressWarnings(plotGenes(genes.up.bed,chrom,chromstart,chromend ,
types=genes.up.bed$type,maxrows=10,bheight=0.1,
plotgenetype="arrow",bentline=FALSE,
labeloffset=0.4,fontsize=0.8,arrowlength = 0.025,
labeltext=TRUE, col=colorRampPalette(rev(brewer.pal(12,"Paired")))(nb.cols)))
axis(side=2,labels = FALSE, tick = FALSE)
mtext("gene",side=2,line=3,cex=1,font=2)
dev.off()

[1] "yes"
[1] "yes"

png: 2

[1] "yes"
[1] "yes"

png: 2

[1] "yes"
[1] "yes"

png: 2

[1] "yes"

png: 2

ghits.bedpe$distance.TSS <- apply(ghits.bedpe, 1, function(x){if(x[9]=="+"&x[10]=="+"){abs(as.numeric(x[2])-as.numeric(x[5]))}else if(x[9]=="+"&x[10]=="-"){abs(as.numeric(x[2])-as.numeric(x[6]))}else if(x[9]=="-"&x[10]=="+"){abs(as.numeric(x[3])-as.numeric(x[5]))}else{abs(as.numeric(x[3])-as.numeric(x[6]))}})

options(repr.plot.width=16, repr.plot.height=8)

ggplot(ghits.bedpe, aes(distance.TSS, log_pvaladj,color=gene)) +geom_point()+
  geom_smooth(method=lm, se=FALSE, fullrange=FALSE)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Distance to TSS")

`geom_smooth()` using formula = 'y ~ x'

options(repr.plot.width=16, repr.plot.height=8)

ggplot(ghits.bedpe, aes(distance.TSS, log_pvaladj,color=gene)) +geom_point()+
  geom_smooth(method=lm, se=FALSE, fullrange=FALSE)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Distance to TSS")

`geom_smooth()` using formula = 'y ~ x'

options(repr.plot.width=8, repr.plot.height=8)
ggplot(ghits.bedpe, aes(reorder(gene, distance.TSS, mean), distance.TSS/1000000)) + geom_boxplot() + theme_minimal() +ylab("Distance to TSS (Mb)")+
  theme(axis.title.x=element_blank(),axis.text.x = element_text(angle=60, colour="black", hjust=1, size=15),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))

options(repr.plot.width=8, repr.plot.height=8)
ggplot(ghits.bedpe, aes(reorder(gene, distance.TSS, mean), distance.TSS/1000000)) + geom_boxplot() + theme_minimal() +ylab("Distance to TSS (Mb)")+
  theme(axis.title.x=element_blank(),axis.text.x = element_text(angle=60, colour="black", hjust=1, size=15),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.text.y=element_text(size=20))

ghits.bedpe <- ghits.bedpe %>% filter(gRNA %in% names(table(ghits.bedpe$gRNA)[table(ghits.bedpe$gRNA)>1]))

ghits.bedpe$samplenumber <- as.numeric(as.factor(ghits.bedpe$gene))
ghits.up.bedpe <- ghits.bedpe[which(ghits.bedpe$score>0),]
ghits.down.bedpe <- ghits.bedpe[which(ghits.bedpe$score<0),] 
ghits.down.bedpe$score <- abs(ghits.down.bedpe$score)
genes.up.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.up.bedpe$name))))), genes.bed$gene),]
genes.down.bed <- genes.bed[match(names(table(as.character(as.factor(gsub("^.*_","",ghits.down.bedpe$name))))), genes.bed$gene),]
genes.up.bed <- rbind(genes.up.bed, genes.down.bed)
genes.up.bed <- genes.up.bed %>% distinct() %>% arrange(gene)
gRNA.up.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.up.bedpe$name))))), gRNA.bed$gene),]
gRNA.down.bed <- gRNA.bed[match(names(table(as.character(as.factor(gsub("_.*$","",ghits.down.bedpe$name))))), gRNA.bed$gene),]
gRNA.up.bed <- rbind(gRNA.up.bed, gRNA.down.bed)
gRNA.up.bed <- gRNA.up.bed %>% distinct()

median(ghits.bedpe$distance.TSS)

485634

length(table(ghits.bedpe$gRNA))

21

genes.up.bed

A data.frame: 28 x 8

	chrom	start	stop	gene	score	strand	type	order
	<chr>	<dbl>	<dbl>	<chr>	<chr>	<chr>	<chr>	<int>
55	chr4	40166674	40167831	AC095057.3	.	+	gene	55
125	chr4	44704404	44704965	AC096586.1	.	+	gene	125
124	chr4	44693945	44694386	AC096586.2	.	-	gene	124
110	chr4	43410040	43410937	AC098590.1	.	-	gene	110
85	chr4	41750344	41757341	AC105389.1	.	+	gene	85
68	chr4	40786109	40786710	ARL4AP2	.	+	gene	68
100	chr4	42408372	42657105	ATP8A1	.	-	gene	100
96	chr4	42110852	42152878	BEND4	.	-	gene	96
60	chr4	40335332	40355217	CHRNA9	.	+	gene	60
123	chr4	44682199	44726588	GNPDA2	.	-	gene	123
49	chr4	40020239	40021517	KRT18P25	.	+	gene	49
88	chr4	41872746	41882955	LINC00682	.	-	gene	88
59	chr4	40316484	40330419	LINC02265	.	+	gene	59
67	chr4	40749924	40811184	NSUN7	.	+	gene	67
48	chr4	39973443	39974338	PABPC1P1	.	+	gene	48
44	chr4	39822862	39977956	PDS5A	.	-	gene	44
83	chr4	41744081	41748725	PHOX2B	.	-	gene	83
62	chr4	40423266	40630875	RBM47	.	-	gene	62
101	chr4	42471809	42472380	RPS7P7	.	+	gene	101
99	chr4	42397487	42402487	SHISA3	.	+	gene	99
94	chr4	41990501	42090461	SLC30A9	.	+	gene	94
14	chr4	38790676	38856817	TLR1	.	-	gene	14
15	chr4	38823714	38856817	TLR6	.	-	gene	15
18	chr4	38966743	39032922	TMEM156	.	-	gene	18
91	chr4	41935128	41960803	TMEM33	.	+	gene	91
32	chr4	39498754	39528311	UGDH	.	-	gene	32
22	chr4	39182503	39285810	WDR19	.	+	gene	22
43	chr4	39770080	39771371	ZBTB12BP	.	-	gene	43

pr_range <- data.frame(gene= genes.bed$gene,start= genes.bed$start-200, end= genes.bed$start+200)
whg <- c()
ispr <- c()
whpr <- c()
for (i in 1:nrow(ghits.bedpe)){
    for (j in 1:nrow(pr_range)){
        if((ghits.bedpe$start1[i]>pr_range$start[j] & ghits.bedpe$start1[i]< pr_range$end[j]) | (ghits.bedpe$end1[i]>pr_range$start[j] & ghits.bedpe$end1[i] < pr_range$end[j])){
            ispr <- c(ispr, "Yes")
            whpr <- c(whpr, pr_range$gene[j])
            whg <- c(whg, ghits.bedpe$gRNA[i])
            break()
        } else {
            if(j == nrow(pr_range)){
            ispr <- c(ispr, "No")
            whpr <- c(whpr, "NA")
            whg <- c(whg, ghits.bedpe$gRNA[i])
            }
        }
    }
}
dat <- data.frame(gRNA = whg, gene = whpr, promoter=ispr)
ghits.bedpe$promoter <- dat$gene
ghits.bedpe %>% filter(promoter!="NA")

A data.frame: 3 x 17

chrom1	start1	end1	chrom2	start2	end2	name	score	strand1	strand2	samplenumber	gene	gRNA	log_pvaladj	type	distance.TSS	promoter
<chr>	<int>	<int>	<chr>	<dbl>	<dbl>	<chr>	<dbl>	<chr>	<chr>	<dbl>	<chr>	<chr>	<dbl>	<chr>	<dbl>	<chr>
chr4	42397377	42398743	chr4	42397487	42402487	R790_SHISA3	0.6905067398	+	+	20	SHISA3	Region_790	191.839188	up_regulated	110	SHISA3
chr4	42397377	42398743	chr4	38823714	38856817	R790_TLR6	-0.0001907844	+	-	23	TLR6	Region_790	3.368763	down_regulated	3540560	SHISA3
chr4	42397377	42398743	chr4	39498754	39528311	R790_UGDH	-0.0018959126	+	-	26	UGDH	Region_790	3.368763	down_regulated	2869066	SHISA3

pr_range <- data.frame(gene= genes.bed$gene,start= genes.bed$start-200, end= genes.bed$start+200)
whg <- c()
ispr <- c()
whpr <- c()
for (i in 1:nrow(ghits.bedpe)){
    for (j in 1:nrow(pr_range)){
        if((ghits.bedpe$start1[i]>pr_range$start[j] & ghits.bedpe$start1[i]< pr_range$end[j]) | (ghits.bedpe$end1[i]>pr_range$start[j] & ghits.bedpe$end1[i] < pr_range$end[j])){
            ispr <- c(ispr, "Yes")
            whpr <- c(whpr, pr_range$gene[j])
            whg <- c(whg, ghits.bedpe$gRNA[i])
            break()
        } else {
            if(j == nrow(pr_range)){
            ispr <- c(ispr, "No")
            whpr <- c(whpr, "NA")
            whg <- c(whg, ghits.bedpe$gRNA[i])
            }
        }
    }
}
dat <- data.frame(gRNA = whg, gene = whpr, promoter=ispr)
ghits.bedpe$promoter <- dat$gene
ghits.bedpe %>% filter(promoter!="NA")

A data.frame: 3 x 17

chrom1	start1	end1	chrom2	start2	end2	name	score	strand1	strand2	samplenumber	gene	gRNA	log_pvaladj	type	distance.TSS	promoter
<chr>	<int>	<int>	<chr>	<dbl>	<dbl>	<chr>	<dbl>	<chr>	<chr>	<dbl>	<chr>	<chr>	<dbl>	<chr>	<dbl>	<chr>
chr4	42397377	42398743	chr4	42397487	42402487	R790_SHISA3	0.6905067398	+	+	20	SHISA3	Region_790	191.839188	up_regulated	110	SHISA3
chr4	42397377	42398743	chr4	38823714	38856817	R790_TLR6	-0.0001907844	+	-	23	TLR6	Region_790	3.368763	down_regulated	3540560	SHISA3
chr4	42397377	42398743	chr4	39498754	39528311	R790_UGDH	-0.0018959126	+	-	26	UGDH	Region_790	3.368763	down_regulated	2869066	SHISA3

Jumpe genes (region)

ghits.bedpe$distance.TSS <- apply(ghits.bedpe, 1, function(x){if(x[9]=="+"&x[10]=="+"){abs(as.numeric(x[2])-as.numeric(x[5]))}else if(x[9]=="+"&x[10]=="-"){abs(as.numeric(x[2])-as.numeric(x[6]))}else if(x[9]=="-"&x[10]=="+"){abs(as.numeric(x[3])-as.numeric(x[5]))}else{abs(as.numeric(x[3])-as.numeric(x[6]))}})

pr_range <- data.frame(gene= genes.bed$gene,start= genes.bed$start-200, end= genes.bed$start+200)
whg <- c()
ispr <- c()
whpr <- c()
for (i in 1:nrow(ghits.bedpe)){
    for (j in 1:nrow(pr_range)){
        if((ghits.bedpe$start1[i]>pr_range$start[j] & ghits.bedpe$start1[i]< pr_range$end[j]) | (ghits.bedpe$end1[i]>pr_range$start[j] & ghits.bedpe$end1[i] < pr_range$end[j])){
            ispr <- c(ispr, "Yes")
            whpr <- c(whpr, pr_range$gene[j])
            whg <- c(whg, ghits.bedpe$gRNA[i])
            break()
        } else {
            if(j == nrow(pr_range)){
            ispr <- c(ispr, "No")
            whpr <- c(whpr, "NA")
            whg <- c(whg, ghits.bedpe$gRNA[i])
            }
        }
    }
}
dat <- data.frame(gRNA = whg, gene = whpr, promoter=ispr)
ghits.bedpe$promoter <- dat$gene

length(unique(TAP_DE$gene))

59

unique(TAP_DE$gene)

1. 'GNPDA2'
2. 'RPS7P7'
3. 'CHRNA9'
4. 'KLHL5'
5. 'AC095057.3'
6. 'PHOX2B'
7. 'AC096586.1'
8. 'AC079921.2'
9. 'BEND4'
10. 'TLR1'
11. 'WDR19'
12. 'RBM47'
13. 'GUF1'
14. 'TMEM33'
15. 'SMIM14'
16. 'KRT18P25'
17. 'FAM114A1'
18. 'AC105389.1'
19. 'ATP8A1'
20. 'APBB2'
21. 'TLR6'
22. 'AC108471.2'
23. 'AC106052.1'
24. 'NSUN7'
25. 'AC096586.2'
26. 'NDUFB4P12'
27. 'LINC02265'
28. 'AC098591.1'
29. 'AC098591.2'
30. 'ARL4AP2'
31. 'RFC1'
32. 'DCAF4L1'
33. 'N4BP2'
34. 'AC096734.1'
35. 'LINC00682'
36. 'PDS5A'
37. 'SLC30A9'
38. 'TMEM156'
39. 'LIAS'
40. 'SHISA3'
41. 'LIMCH1'
42. 'PABPC1P1'
43. 'AC021148.1'
44. 'ATP1B1P1'
45. 'UBE2K'
46. 'ZBTB12BP'
47. 'UCHL1.AS1'
48. 'AC105389.3'
49. 'UCHL1'
50. 'AC096734.2'
51. 'AC024022.1'
52. 'RPL12P20'
53. 'YIPF7'
54. 'UGDH'
55. 'AC098590.1'
56. 'TLR10'
57. 'LINC02475'
58. 'AC108210.1'
59. 'AC111006.1'

Only coding genes

ghits.bedpe.coding <- ghits.bedpe %>% filter( gene %in% coding_genes)

genes.bed.detected <- genes.bed[genes.bed$gene %in% coding_genes,] 
jumped_gene_counts <- c()
count <- 0
for (i in 1:nrow(ghits.bedpe.coding)){
    for (j in 1:nrow(genes.bed.detected)){
        if(genes.bed.detected$start[j]>=min(c(ghits.bedpe.coding$start1[i],ghits.bedpe.coding$start2[i],ghits.bedpe.coding$end1[i],ghits.bedpe.coding$end2[i])) & genes.bed.detected$stop[j]<=max(c(ghits.bedpe.coding$start1[i],ghits.bedpe.coding$start2[i],ghits.bedpe.coding$end1[i],ghits.bedpe.coding$end2[i])) & ghits.bedpe.coding$gene[i]!=genes.bed.detected$gene[j]){
            count <- count + 1
        }
        if(j == nrow(genes.bed.detected)){
                jumped_gene_counts <- c(jumped_gene_counts, count)
            count <- 0
        }
   }
}
table(jumped_gene_counts)

jumped_gene_counts
 0  2  3  8  9 10 12 14 15 20 21 22 23 
18  4  2  1  1  1  1  1  1  1  1  1  1 

## Skipped genes
length(jumped_gene_counts)-18

16

ghits.bedpe.coding$jumped_gene_counts <- jumped_gene_counts

options(repr.plot.width=8, repr.plot.height=8)
ggplot(ghits.bedpe.coding, aes(jumped_gene_counts, log_pvaladj)) +geom_point(aes(colour = score),size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Number of coding genes jumped")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
labs(color="avg_logFC")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)+ scale_color_gradient2(low = "blue", mid = "#dddeee", high = "red", midpoint = 0)

pdf("Coding_genes_jumped_region_with_logFC_pval_202502.pdf",width=8,height=6)
ggplot(ghits.bedpe.coding, aes(jumped_gene_counts, log_pvaladj)) +geom_point(aes(colour = score),size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Number of coding genes jumped")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
labs(color="avg_logFC")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)+ scale_color_gradient2(low = "blue", mid = "#dddeee", high = "red", midpoint = 0)
dev.off()

png: 2

ggplot(data.frame(table(jumped_gene_counts)), aes(x=jumped_gene_counts, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("Coding genes jumped")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )

pdf("Coding_genes_jumped_region_202502.pdf",width=6,height=6)
ggplot(data.frame(table(jumped_gene_counts)), aes(x=jumped_gene_counts, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("Coding genes jumped")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()

png: 2

Only Non-coding genes/ Pseudogenes considered

ghits.bedpe.ncoding <- ghits.bedpe %>% filter( gene %in% non_coding_genes)

genes.bed.detected <- genes.bed[genes.bed$gene %in% non_coding_genes,] 
jumped_gene_counts <- c()
count <- 0
for (i in 1:nrow(ghits.bedpe.ncoding)){
    for (j in 1:nrow(genes.bed.detected)){
        if(genes.bed.detected$start[j]>=min(c(ghits.bedpe.ncoding$start1[i],ghits.bedpe.ncoding$start2[i],ghits.bedpe.ncoding$end1[i],ghits.bedpe.ncoding$end2[i])) & genes.bed.detected$stop[j]<=max(c(ghits.bedpe.ncoding$start1[i],ghits.bedpe.ncoding$start2[i],ghits.bedpe.ncoding$end1[i],ghits.bedpe.ncoding$end2[i])) & ghits.bedpe.ncoding$gene[i]!=genes.bed.detected$gene[j]){
            count <- count + 1
        }
        if(j == nrow(genes.bed.detected)){
                jumped_gene_counts <- c(jumped_gene_counts, count)
            count <- 0
        }
   }
}
table(jumped_gene_counts)

jumped_gene_counts
 0  4  5  7  9 10 11 12 16 17 
 5  3  1  1  1  1  1  1  3  1 

## Skipped genes
length(jumped_gene_counts)-5

13

ghits.bedpe.ncoding$jumped_gene_counts <- jumped_gene_counts

options(repr.plot.width=8, repr.plot.height=8)
ggplot(ghits.bedpe.ncoding, aes(jumped_gene_counts, log_pvaladj)) +geom_point(aes(colour = score),size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Number of non-coding/pseudo genes jumped")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
labs(color="avg_logFC")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)+ scale_color_gradient2(low = "blue", mid = "#dddeee", high = "red", midpoint = 0)

pdf("Non_coding_genes_jumped_region_with_logFC_pval_202502.pdf",width=8,height=6)
ggplot(ghits.bedpe.ncoding, aes(jumped_gene_counts, log_pvaladj)) +geom_point(aes(colour = score),size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Number of non-coding/pseudo genes jumped")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
labs(color="avg_logFC")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)+ scale_color_gradient2(low = "blue", mid = "#dddeee", high = "red", midpoint = 0)
dev.off()

png: 2

ggplot(data.frame(table(jumped_gene_counts)), aes(x=jumped_gene_counts, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("Non-coding/pseudo genes jumped")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )

pdf("Non_coding_pseudo_genes_jumped_region_202502.pdf",width=6,height=6)
ggplot(data.frame(table(jumped_gene_counts)), aes(x=jumped_gene_counts, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("Non-coding/pseudo genes jumped")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()

png: 2

All genes considered

genes.bed.detected <- genes.bed[genes.bed$gene %in% unique(TAP_DE$gene),] 
jumped_gene_counts <- c()
count <- 0
for (i in 1:nrow(ghits.bedpe)){
    for (j in 1:nrow(genes.bed.detected)){
        if(genes.bed.detected$start[j]>=min(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & genes.bed.detected$stop[j]<=max(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & ghits.bedpe$gene[i]!=genes.bed.detected$gene[j]){
            count <- count + 1
        }
        if(j == nrow(genes.bed.detected)){
                jumped_gene_counts <- c(jumped_gene_counts, count)
            count <- 0
        }
   }
}
table(jumped_gene_counts)

jumped_gene_counts
 0  1  2  3  4  6  7  9 14 17 18 19 21 23 24 26 28 29 34 42 43 45 
13  7  2  1  2  1  3  4  1  1  1  3  1  1  2  1  1  2  1  1  2  1 

## Skipped genes
length(jumped_gene_counts)-13

39

options(repr.plot.width=8, repr.plot.height=8)
boxplot(jumped_gene_counts, main="number of jumped genes", cex.lab=1.5)
summary(jumped_gene_counts)

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   0.00    0.75    6.50   11.58   19.50   45.00 

ghits.bedpe$jumped_gene_counts <- jumped_gene_counts

options(repr.plot.width=8, repr.plot.height=8)
ggplot(ghits.bedpe, aes(jumped_gene_counts, log_pvaladj)) +geom_point(aes(colour = score),size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Number of genes jumped")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
labs(color="avg_logFC")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)+ scale_color_gradient2(low = "blue", mid = "#dddeee", high = "red", midpoint = 0)

pdf("Genes_jumped_region_with_logFC_pval_202407.pdf",width=8,height=6)
ggplot(ghits.bedpe, aes(jumped_gene_counts, log_pvaladj)) +geom_point(aes(colour = score),size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Number of genes jumped")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 16))+
labs(color="avg_logFC")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)+ scale_color_gradient2(low = "blue", mid = "#dddeee", high = "red", midpoint = 0)
dev.off()

png: 2

ggplot(data.frame(table(jumped_gene_counts)), aes(x=jumped_gene_counts, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("Genes jumped")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )

pdf("Genes_jumped__region_202212.pdf",width=6,height=6)
ggplot(data.frame(table(jumped_gene_counts)), aes(x=jumped_gene_counts, y=Freq)) + 
  geom_bar(stat = "identity")+theme_classic()+xlab("Genes jumped")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()

png: 2

ghits.bedpe$jumped_gene_counts <- jumped_gene_counts
sig <- c()
count <- 0
sig_ratio <- c()
for (i in 1:nrow(ghits.bedpe)){
    for (j in 1:nrow(genes.bed.detected)){
        if(genes.bed.detected$start[j]>=min(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & genes.bed.detected$stop[j]<=max(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & ghits.bedpe$gene[i]!=genes.bed.detected$gene[j]){
            count <- count + 1
            sig <- c(sig, if(as.numeric(TAP_DE$p_val_adj[which(TAP_DE$gene == genes.bed.detected$gene[j] & TAP_DE$ident == ghits.bedpe$gRNA[i])])<0.01){"sig"}else{"non_sig"})
        }
        if(j == nrow(genes.bed.detected)){
            sig_ratio <- c(sig_ratio, if(count==0){1}else{length(which(sig=="sig"))/length(sig)})
            sig <- c()
            count <- 0
        }
   }
}
ghits.bedpe$sig_ratio <- sig_ratio

options(repr.plot.width=9.5, repr.plot.height=8)
ggplot(ghits.bedpe, aes(jumped_gene_counts, log_pvaladj))+ geom_point(aes(colour = sig_ratio),size=4) + theme_minimal() + xlab("Genes jumped") + ylab("-log adjusted p-value") + 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 20))+
labs(color="Fraction\nsignificant\ngRNAs")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

options(repr.plot.width=9.5, repr.plot.height=8)
ggplot(ghits.bedpe, aes(jumped_gene_counts, log_pvaladj))+ geom_point(size=4) + theme_minimal() + xlab("Genes jumped") + ylab("-log adjusted p-value") + 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 20))+
labs(color="Fraction\nsignificant\ngRNAs")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

pdf("Genes_jumped_vs_pvalue_region_202212.pdf",width=6,height=6)
ggplot(ghits.bedpe, aes(jumped_gene_counts, log_pvaladj))+ geom_point(size=4) + theme_minimal() + xlab("Genes jumped") + ylab("-log adjusted p-value") + 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 20))+
labs(color="Fraction\nsignificant\ngRNAs")+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)
dev.off()

png: 2

jumped_gene_counts <- c()
LFC <- c()
LFC_diff <- c()
for (i in 1:nrow(ghits.bedpe)){
    for (j in 1:nrow(genes.bed.detected)){
        if(genes.bed.detected$start[j]>=min(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & genes.bed.detected$stop[j]<=max(c(ghits.bedpe$start1[i],ghits.bedpe$start2[i],ghits.bedpe$end1[i],ghits.bedpe$end2[i])) & ghits.bedpe$gene[i]!=genes.bed.detected$gene[j]){
            LFC <- c(LFC, if(!is.na(as.numeric(TAP_DE$avg_logFC[which(TAP_DE$gene == genes.bed.detected$gene[j] & TAP_DE$ident == ghits.bedpe$gRNA[i])]))){as.numeric(TAP_DE$avg_logFC[which(TAP_DE$gene == genes.bed.detected$gene[j] & TAP_DE$ident == ghits.bedpe$gRNA[i])])})
        }
        if(j == nrow(genes.bed.detected)){
            LFC_diff <- c(LFC_diff, sum(ghits.bedpe$score[i]-LFC)/length(LFC))
            LFC <- c()
        }
   }
}

length(LFC_diff)
sum(is.na(LFC_diff))

52

16

ggplot(data.frame(LFC_diff), aes(x=LFC_diff)) + 
  geom_histogram()+theme_classic()+xlab("LFC (target genes vs. jumped genes)")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )

`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning message:
“Removed 16 rows containing non-finite values (`stat_bin()`).”

pdf("LFC_target_vs_jumped_region_202212.pdf",width=6,height=6)
ggplot(data.frame(LFC_diff), aes(x=LFC_diff)) + 
  geom_histogram()+theme_classic()+xlab("LFC (target genes vs. jumped genes)")+ylab("Counts")+
  theme(axis.text.x = element_text(size=12),axis.text.y=element_text(size=12),plot.title = element_text(size=20),
        axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20))+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
      )
dev.off()

`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning message:
“Removed 16 rows containing non-finite values (`stat_bin()`).”

png: 2

hist(LFC_diff, main = "", xlab="LFC target genes vs. jumped genes", ylab="Counts", cex.lab=1.5, breaks=30)

ghits.bedpe$LFC_diff <- LFC_diff

options(repr.plot.width=8, repr.plot.height=8)
ggplot(ghits.bedpe, aes(LFC_diff, log_pvaladj))+ geom_point(size=4)+ theme_minimal() + xlab("LFC target genes vs. jumped genes") + ylab("-log adjusted p-value") + 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20))+
                                    theme_classic()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)

Warning message:
“Removed 16 rows containing missing values (`geom_point()`).”

options(repr.plot.width=8, repr.plot.height=8)
ggplot(ghits.bedpe, aes(distance.TSS, log_pvaladj)) +geom_point(size=4)+theme_minimal()+ylab("-log(adj_p_value)")+xlab("Distance to TSS")+ 
  theme(axis.text.x = element_text(size=20),axis.text.y = element_text(size=16),axis.title.x=element_text(margin = margin(t = 20, r = 0, b = 0, l = 0),size=20),axis.title.y=element_text(margin = margin(t = 0, r = 20, b = 0, l = 0),size=20),legend.title=element_text(size=20),legend.text = element_text(size = 20))+
labs(color="Fraction\nsignificant\ngRNAs")+
                                    theme_classic()+
  theme(
    panel.background = element_rect(fill = "transparent", colour = NA),
    plot.background = element_rect(fill = "transparent", colour = NA),
    legend.background = element_rect(fill = "transparent", colour = NA),
    legend.box.background = element_rect(fill = "transparent", colour = NA,)
)